A study of elective genome sequencing and pharmacogenetic testing in an unselected population

Meagan Cochran; Kelly East; Veronica Greve; Melissa Kelly; Whitley Kelley; Troy Moore; Richard M Myers; Katherine Odom; Molly C Schroeder; David Bick

doi:10.1002/mgg3.1766

. 2021 Jul 27;9(9):e1766. doi: 10.1002/mgg3.1766

A study of elective genome sequencing and pharmacogenetic testing in an unselected population

Meagan Cochran ¹, Kelly East ¹, Veronica Greve ¹, Melissa Kelly ¹, Whitley Kelley ¹, Troy Moore ², Richard M Myers ¹, Katherine Odom ¹, Molly C Schroeder ³, David Bick ^1,^✉

PMCID: PMC8457704 PMID: 34313030

Abstract

Background

Genome sequencing (GS) of individuals without a medical indication, known as elective GS, is now available at a number of centers around the United States. Here we report the results of elective GS and pharmacogenetic panel testing in 52 individuals at a private genomics clinic in Alabama.

Methods

Individuals seeking elective genomic testing and pharmacogenetic testing were recruited through a private genomics clinic in Huntsville, AL. Individuals underwent clinical genome sequencing with a separate pharmacogenetic testing panel.

Results

Six participants (11.5%) had pathogenic or likely pathogenic variants that may explain one or more aspects of their medical history. Ten participants (19%) had variants that altered the risk of disease in the future, including two individuals with clonal hematopoiesis of indeterminate potential. Forty‐four participants (85%) were carriers of a recessive or X‐linked disorder. All individuals with pharmacogenetic testing had variants that affected current and/or future medications.

Conclusion

Our study highlights the importance of collecting detailed phenotype information to interpret results in elective GS.

Keywords: carrier, clonal hematopoiesis of indeterminate potential, elective genome, pharmacogenetics

Genome sequencing (GS) of individuals without a medical indication is referred to as elective GS. Among 52 individuals undergoing elective GS, 11.5% (6/52) had pathogenic or likely pathogenic variants that may explain one or more aspects of their medical history, 19% (10/52) had variants that altered the risk of disease in the future, including two individuals with clonal hematopoiesis of indeterminate potential, 85% (44/52) were carriers of a recessive or X‐linked disorder, and 100% of individuals with pharmacogenetic testing had variants that affected current and/or future medications.

1. INTRODUCTION

Genome sequencing (GS) has entered clinical practice as an efficient approach to the diagnosis of rare genetic disorders (Bick et al., 2019). However, interest in this testing is not limited to patients with a medical indication for testing. Individuals without a medical indication request a variety of genetic tests, including GS. Such testing is referred to as “elective” genetic and genomic testing (https://en.wikipedia.org/wiki/Elective_genetic_and_genomic_testing; Lu et al., 2019).

Elective testing uses GS or exome sequencing (ES) to evaluate an individual for both primary findings and secondary findings. Primary findings include variants that purport to explain an aspect of the patient's medical or family history. Secondary findings are variants that do not appear to be associated with medical or family history at the time of testing but are nevertheless clinically relevant. Examples of secondary findings include a pathogenic BRCA1 (*113705) variant in an individual with no known personal or family history of breast/ovarian cancer and carrier status for an autosomal recessive condition for which there is no known family history.

The frequency and nature of the primary and secondary findings reported in elective genome studies have been quite variable for a number of reasons (Table A1). Patient recruitment criteria were not uniform across studies. For example, all study subjects were provided testing for free as part of a research project except those reported by Hou et al. (2020). In addition, the list of genes analyzed and criteria used for variant classification varied across studies. Since the first papers describing the use of elective genomic testing were published in 2012, the knowledge base concerning the association between genetic variants and human disease has grown significantly with the development of resources such as ClinVar, ClinGen, and gnomAD. As a result, recent elective testing produces more clinically relevant findings than did earlier testing. Further, while all elective GS and ES studies correlated variants with medical history, family history was not always considered. Some participants were likely motivated to undertake elective testing due to a suspected genetic disorder in the family. Considering these factors, it is unsurprising that studies examining patient perceptions and economic aspects of elective genomic testing yield a range of results and recommendations (Baptista et al., 2016; East et al., 2019; Fiala et al., 2019; Flemin et al., 2019; Lewis et al., 2016; Lupo et al., 2016; Price et al., 2017; Roberts et al., 2018; Sanderson et al., 2016; Zoltick et al., 2019).

TABLE 1.

Variants reported by elective clinical genome sequencing.

Participant information				Variant information
Insight number	Age	Sex	ICD10	Variant category	Gene	Transcript		Variant (genomic)	Variant (coding)	Variant (protein)	Variant classification
1	55	F	Oth Disorders Of Plasma‐Protein Metabolism, Nec E88.09 Sleep Apnea, Unspecified G47.30 Restless Legs Syndrome G25.81 Dysthymic Disorder F34.1	Pharmacogenetic	BCHE	NM_024006.5		chr3:g.165547569G>T	1253G>T	NA	NA
1	55	F		Secondary Carrier	CNGB3	NM_019098		chr8:g.87656009delG	1148delC	T383Ifs*13	Pathogenic
2	69	F	Giant Cell Arteritis With Polymyalgia Rheumatica M31.5	Secondary Carrier	BBS1	NM_024649		chr11:g.66293652T>G	1169T>G	M390R	Pathogenic
				Secondary Carrier	RNASEH2B	NM_024570		chr13:g.51519581G>A	529G>A	A177T	Pathogenic
				Secondary Carrier	TACR3	NM_001059		chr4:g.104577415C>T	824G>A	W275*	Likely Pathogenic
3	51	F	Hypothyroidism, Unspecified E03.9	no reportable variants identified
4	32	F	Attention‐Deficit Hyperactivity Disorder, Unspecified Type F90.9	Secondary Carrier	PCDH15	NM_001142768		chr10:g.55698574C>T	NA	NA	Pathogenic
5	63	F	Eosinophilic Esophagitis K20.0 Dysthymic Disorder F34.1	Secondary Carrier	GCDH	NM_000159		chr19:g.13010300C>T	1262C>T	A421V	Pathogenic
				Secondary Carrier	CLCN1	NM_000083		chr7:g.143048771C>T	2680C>T	R894*	Pathogenic
				Secondary Disease	ASB10	NM_001142460		chr7:g.150884003C>T	215G>A	R72H	Pathogenic
6	73	F	Parkinson's Disease G20 Abnormal Weight Loss R63.4 Unspecified Age‐Related Cataract H25.9 Unspecified Sensorineural Hearing Loss H90.5 Unspecified Dementia Without Behavioral Disturbance F03.90	no reportable variants identified
7	74	M	Malignant Neoplasm Of Prostate C61 Low Back Pain M54.5 Unspecified Atrial Fibrillation I48.91 Dvrtclos Of Lg Int W/o Perforation Or Abscess W Bleeding K57.31 Unspecified Abdominal Hernia Without Obstruction Or Gangrene K46.9 Gilbert Syndrome E80.4 Polyp Of Colon K63.5 Cortical Age‐Related Cataract, Unspecified Eye H25.019 Endothelial Corneal Dystrophy H18.51	Primary	MSR1	NM_138715		chr8:g.16012590C>T	881G>A	G294E	VUS
7	74	M		Secondary Carrier	SERPIN A1	NM_001002236		chr14:g.94844947C>T	1096G>A	E366K	Pathogenic
8	59	F	Exercise Induced Bronchospasm J45.990 Celiac Disease K90.0	Secondary Carrier	GPSM2	NM_013296		chr1:g.109466682C>A	1661C>A	S554*	Likely Pathogenic
9	81	M	Malignant Neoplasm Of Prostate C61 Unspecified Sensorineural Hearing Loss H90.5 Unspecified Cataract H26.9 Frequency Of Micturition R35.0	Primary	MSR1	NM_138715		chr8:g.16012590C>T	881G>A	G294E	VUS
				Secondary Carrier	SLC45A 2	NM_001012509		chr5:g.33951658C>G	NA	NA	Likely Pathogenic
				Secondary Carrier	GALC	NM_000153		chr14:g.88452941T>C	334A>G	T112A	Likely Pathogenic
10	79	M	Age‐Related Cognitive Decline R41.81 Unspecified Age‐Related Cataract H25.9 Low Back Pain M54.5 Pain In Unspecified Hip M25.559 Other Chronic Sinusitis J32.8	no reportable variants identified
11	57	F	Syncope And Collapse R55 Renal Agenesis, Unilateral Q60.0 Congenital Absence Of Ovary, Unilateral Q50.01	Primary	NKX2‐5		NM_001166176	chr5:g.172660374C>T	428G>A	R143Q	VUS
12	59	M	Old Myocardial Infarction I25.2 Tinea Unguium B35.1 Other Intervertebral Disc Displacement, Lumbar Region M51.26 Sleep Apnea, Unspecified G47.30 Hyperlipidemia, Unspecified E78.5 Essential (primary) Hypertension I10 Polyp Of Colon K63.5	Secondary Carrier	HFE		NM_000410	chr6:g.26093141G>A	845G>A	C282Y	Pathogenic
12	59	M		Secondary Carrier	GAA		NM_000152	chr17:g.78078341T>G	NA	NA	Pathogenic
13	57	F	Oth Types Of Non‐Hodg Lymph, Nodes Of Head, Face, And Neck C85.81 Hyperlipidemia, Unspecified E78.5 Hypothyroidism, Unspecified E03.9 Acute Embolism And Thrombosis Of Other Thoracic Veins I82.290	Primary	F5		NM_000130	chr1:g.169519049T>C	1601A>G	Q534R	Pathogenic
				Primary	PRF1		NM_001083116	chr10:g.72357895delG	1582delC	H528Tfs*85	Likely Pathogenic
				Secondary Carrier	SERPIN A1		NM_001127701	chr14:g.94847262T>A	863A>T	E288V	Pathogenic
				Secondary Carrier	MVK		NM_000431	chr12:g.110024570C>T	643C>T	R215*	Pathogenic
				Secondary Carrier	TMPRSS3		NM_024022	chr21:g.43795896C>T	1276G>A	A426T	Likely Pathogenic
14	53	M	Chronic Ischemic Heart Disease, Unspecified I25.9 Essential (primary) Hypertension I10 Hyperlipidemia, Unspecified E78.5 Gastro‐Esophageal Reflux Disease Without Esophagitis K21.9 Anodontia K00.0	Primary	WNT10A		NM_025216	chr2:g.219755011T>A	682T>A	F228I	Pathogenic
				Secondary Carrier	PYGM		NM_001164716	chr11:g.64527223G>A	148C>T	R50*	Pathogenic
				Secondary Carrier	TYR		NM_000372	chr11:g.89017973C>T	1217C>T	P406L	Pathogenic
				Secondary Carrier	ATM		NM_000051	chr11:g.108121753_108 121754delAG	1561_1562delAG	E522Ifs*43	Pathogenic
15	31	M	Acne Vulgaris L70.0 Mild Intermittent Asthma, Uncomplicated J45.20 Tension‐Type Headache, Unspecified, Not Intractable G44.209	Pharmacogenetic	TPMT		NM_000367.3	chr6:g.18130918T>C	c.719A>G	NA	NA
				Pharmacogenetic	TPMT		NM_000367.3	chr6:g. 18139228C>T	c.460G>A	NA	NA
				Pharmacogenetic	NUDT15		NM_018283.3	chr13:g.48619855C>T	c.415C>T	NA	NA
16	61	M	Gastro‐Esophageal Reflux Disease Without Esophagitis K21.9 Essential (primary) Hypertension I10 Obstructive Sleep Apnea (adult) (pediatric) G47.33	Secondary Carrier	ACADM		NM_000016.5	chr1:g. 76226846A>G	c.985A>G	p.Lys329Glu	Pathogenic
				Secondary Carrier	C5orf42		NM_023073.3	chr5:g. 37226878delA	c.1819delT	p.Tyr607ThrfsTer6	Likely Pathogenic
				Secondary Carrier	COL4A3		NM_000091.4	chr2:g. 228176554C>T	c.4981C>T	p.Arg1661Cys	Likely Pathogenic
				Secondary Carrier	JAGN1		NM_032492.3	chr3:g. 9932409G>A	c.3G>A	p.Met1?	Pathogenic
				Secondary Carrier	WDR72		NM_182758.3	chr15:g. 54003546G>A	c.844C>T	p.Gln282Ter	Likely Pathogenic
17	34	F	Anxiety Disorder, Unspecified F41.9 Hypothyroidism, Unspecified E03.9 Attention‐Deficit Hyperactivity Disorder, Unspecified Type F90.9	no reportable variants identified
18	51	M	Pure Hypercholesterolemia, Unspecified E78.00 Essential (primary) Hypertension I10 Disorder Of Bilirubin Metabolism, Unspecified E80.7 Allergy To Peanuts Z91.010	Secondary Carrier	MTFMT	NM_139242.3		chr15:g. 65313871G>A	c.626C>T	p.Ser209Leu	Pathogenic
18	51	M		Secondary Carrier	SERPINA1	NM_000295.4		chr14:g. 94847262T>A	c.863A>T	p.Glu288Val	Likely Pathogenic
19	35	F	Calculus Of Kidney N20.0	Primary	CYP24A1	NM_000782.4		chr20:g. 52788190G>A	c.469C>T	p.Arg157Trp	VUS
				Secondary Carrier	HFE	NM_000410.3		chr6:g.26093141G>A	c.845G>A	p.Cys282Tyr	Pathogenic
				Secondary Carrier	RNASEH2B	NM_024570.3		chr13:g.51519581G>A	c.529G>A	p.Ala177Thr	Pathogenic
				Secondary Carrier	SLC26A3	NM_000111.2		chr7:g. 107412534_1074 12535insTGA	c.2026_2027dupTCA	p.Ile675dup	Likely Pathogenic
				Secondary Carrier	WRAP53	NM_018081.2		chr17:g. 7591983_75919 84delCT	c.17_18delCT	p.Gln7ThrfsTer27	Likely Pathogenic
20	49	M	Essential (primary) Hypertension I10	Secondary Carrier	FGB	NM_005141.4		chr4:g. 155486984C>T	c.139C>T	p.Arg47Ter	Pathogenic
				Secondary Carrier	IDUA	NM_000203.4		chr4:g. 996535G>A	c.1205G>A	p.Trp402Ter	Pathogenic
				Secondary Carrier	TG	NM_003235.4		chr8:g. 133894854C>T	c.886C>T	p. Arg296Ter	Pathogenic
21	44	F	Eclampsia Complicating The Puerperium O15.2 Malignant Neoplasm Of Unsp Site Of Unspecified Female Breast C50.919 Supraventricular Tachycardia I47.1	Secondary Carrier	AGXT	NM_000030.2		chr2:g. 241808773C>T	c.352C>T	p.p.Arg118Cys	Likely Pathogenic
				Secondary Carrier	CBS	NM_000071.2		chr21:g. 44478972C>T	c.1330G>A	p. Asp444Asn	Likely Pathogenic
				Secondary Carrier	DHCR7	NM_001360.2		chr11:g. 71146886C>G	c.964‐1G>C	NA	Pathogenic
				Secondary Carrier	G6PD	NM_000402.4		chrX:g. 153760649C>G	c.1406G>C	p.Arg469Pro	Likely Pathogenic
22	46	M	Neoplasm Of Uncertain Behavior Of Connctv/soft Tiss D48.1	no reportable variants identified
23	63	M	Persistent Atrial Fibrillation I48.1 Noise Effects On Left Inner Ear H83.3X2	Secondary Carrier	CYP17A1	NM_000102.3		chr10:g. 104596941_104 596942insT	c.177dupA	p.Tyr60IlefsTer29	Likely Pathogenic
23	63	M		Secondary Disease	WNT10A	NM_025216.2		chr2:g. 219755011T>A	c.682T>A	p.Phe228Ile	Pathogenic
24	74	M	Rheumatoid arthritis M05.89 Onychomycosis B35.1 Gallstones K80.0 Kidney stones N20.0	Primary	CLEC7A	NM_197947		chr12:g.10271087A>C	714T>G	Y238*	VUS
				Secondary Carrier	GAA	NM_001079804		chr17:g.78078341T>G	NA	NA	Pathogenic
				Secondary Carrier	USH2A	NM_007123		chr1:g.216497582C>A	1256G>T	C419F	Pathogenic
				Pharmacogenetic	TMPT*3A	NM_000367.3		chr6:18130918A>G	c.719A>G	NA	NA
				Pharmacogenetic	TMPT*3A	NM_000367.3		chr6:1139228G>A	c.460G>A	NA	NA
				Pharmacogenetic	CYP2D6*6	NM_000769.2		chr22:42525086delT	c. 454delT	NA	NA
				Pharmacogenetic	CYP2C19*17	NM_000769.2		chr10:96521657C>T	c.−806C>T	NA	NA
				Pharmacogenetic	UGT1A1*80	NM_019075.2		chr2:234668570C>T	c.−364C>T	NA	NA
25	71	F	Major Depressive Disorder F33.9 Interstitial Pulmonary Disease J84.9	Secondary Carrier	MED25	NM_030973.3		chr19:g. 50334047C>T	c.1004C>T	p.Ala335Val	Likely Pathogenic
26	59	M	Paroxysmal Atrial Fibrillation I48.0 Essential Hypertension I10 Behign Neoplasm of Cerebral Meninges D32.0	Secondary Disease	WNT10A	NM_025216.2		chr2:g. 219755011T>A	c.682T>A	p.Phe228Ile	Likely Pathogenic
27	62	M	Benign prostatic hypertrophy N40.1 Age‐related cognitive decline R41.84	Secondary Disease	APOC3	NM_000040.1		chr11:g. 116701354G>A	c.55+1G>A	NA	Pathogenic
				Secondary Carrier	GJB2	NM_004004.5		chr13:g. 20763686delC	c.35delG	p.Gly12ValfsTer2	Pathogenic
				Secondary Carrier	LOXHD1	NM_144612.6		chr18:g. 44109190G>A	c.4480C>T	p.Arg1494Ter	Pathogenic
				Pharmacogenetic	CYP2C19	NM_000769.2		chr10:g.96541616G>A	c.19154G>A	NA	NA
				Pharmacogenetic	SLCO1B1	NM_006446.4		chr12:g.21331549T>C	c.521T>C	NA	NA
				Pharmacogenetic	VKORC1	NM_024006. 5		chr16:g.31107689C>T	c.−1639G>A	NA	NA
28	71	F	Other Specified Forms of Tremor G25.2 Abnormal Head Movements R25.0 Unspecified Voice and Resonance Disorder R49.9 Other Chorea G25.5 Hypothyroidism, Unspecified E03.9 Other Age‐Related Cataract H25.89 Other Muscle Spasm M628.38	Secondary Carrier	TYR	NM_000372.4		chr11:g. 89018126A>G	c.1366+4A>G	NA	Likely Pathogenic
29	70	F	Malignant Neoplasm of Breast C50.919 Family History of Epilepsy and Other Disease of the Nervous System Z82.0	Primary	PER3	NM_001289862.1		chr1:g. 7869953C>G	c.1243C>G	p.Pro415Ala	VUS
				Primary	PER3	NM_001289862.1		chr1:g. 7869960A>G	c.1250A>G	p.His417Arg	VUS
				Secondary Carrier	SERPINA1	NM_000295.4		chr14:g. 94844947C>T	c.1096G>A	p.Glu366Lys	Pathogenic
				Secondary Carrier	SLC7A9	NM_014270.4		chr19:g. 33353427C>T	c.544G>A	p.Ala182Thr	Pathogenic
30	69	F	Primary Osteoarthritis, Right Hand M19.041 Primary Osteoarthritis, Left Hand 19.042 Pure Hypercholesterolemia E78.00 Sensorineural HL, Ulilateral H90.42 Cyclical Vomiting, Not Intractable G43.A0	Secondary Carrier	RSPH1	NM_080860.3		chr21:g. 43906573T>G	c.275‐2A>C	NA	Pathogenic
30	69	F		Secondary Carrier	TACR3	NM_001059.2		chr4:g. 104577415C>T	c.824G>A	p.Trp275Ter	Pathogenic
31	61	M	Pure Hypercholesterolemia, Unspecified E78.00 Essential (primary) Hypertension I10	Secondary Carrier	ACADM	NM_000016.5		chr1:g.76226846A>G	c.985A>G	p.Lys329Glu	Pathogenic
				Secondary Carrier	EVC2	NM_147127.4		chr4:g.5633522G>A	c.1708C>T	p.Gln570Ter	Pathogenic
				Secondary Disease	SLC3A1	NM_000341.3		chr2:g.44539839G>T	c.1447G>T	p.Glu483Ter	Pathogenic
				Secondary Carrier	USH2A	NM_007123.5		chr1:g. 216363622_2163 63623delAG	c.4338_4339delCT	p.Cys1447GlnfsTer29	Pathogenic
				Secondary Carrier	ALG12	NM_024105.3		chr22:g.50307032C>T	c.295+1G>A	NA	Likely Pathogenic
				Secondary Carrier	COL9A1	NM_001851.4		chr6:g.70981381C>A	c.1120G>T	p.Glu374Ter	Likely Pathogenic
32	55	F	Tic Disorder, Unspecified F95.9 Rosacea, Unspecified L71.9 Dry Eye Syndrome H04.129 Cerv Disc Disord M50.020 Raynaud's Syndrome I73.00 Hypothyroidism, Unspecified E03.9 Polyp of Colon K63.5 MIgraine G43.909	Primary	MSH2	NM_000251.2		chr:2g.47637301T>G	c.435T>G	p.Ile145Met	VUS
				Secondary Carrier	AIRE	NM_000383		chr21:g.45711063_45711075delGCCTGTCCCCTCC	c.965_977delGCCTGTCCCCTCC	p.Leu323SerfsTer51	Pathogenic
				Secondary Carrier	CFTR	NM_000492.3		chr7:g.117199645_11719964delTCT	c.1520_1522delTCT	p.Phe508del	Pathogenic
				Secondary Carrier	DMP1	NM_004407.3		chr4:g.88578228G>A	c.99G>A	p.Trp33Ter	Pathogenic
				Secondary Carrier	FANCA	NM_000135.2		chr16:g.89828378_89828379insCAGCTTCAGGTTGAATTTC	c.2830_2831dupGAAATTCAACCTGAAGCTG	p.Asp944GlyfsTer5	Pathogenic
				Secondary Carrier	MYBPC1	NM_002465.3		chr12:g.102071879G>A	c.3110‐1G>A	NA	Likely Pathogenic
33	67	M	Hyperlipidemia, Unspecified E78.5 Circadial Rhythm Sleep Disord G47.20 Unspecified Hearing Loss H91.90	Primary	LIPI	NM_198996.3		chr21:g. 15561623C>T	c.227G>A	p.Cys76Tyr	VUS
				Secondary Disease	APC	NM_000038.5		chr5:g. 112175211T>A	c.3920T>A	p.Ile1307Lys	Likely Pathogenic
				Secondary Carrier	TUBGCP4	NM_014444.4		chr15:g. 43675557_4367 5558insT	c.578insT	p.Gly194TrpfsTer8	Likely Pathogenic
34	67	F	Hyperlipidemia, Unspecified E78.5 Episodic Cluster Headache G44.019 Essential (primary) Hypertension I10	Secondary Carrier	MEFV	NM_000243.2		chr16:g. 3293257C>A	c.2230G>T	p.Ala744Ser	Likely Pathogenic
35	30	M	Anxiety Disorder, Unspecified F41.9 Attention‐Deficit Hyperactivity Disorder, Other Type F90.8	Secondary Carrier	LIG4	NM_002312.3		chr13:g.108862342_108 862346delTCTTT	c.1271_1275delAAAGA	p.Lys424ArgfsTer20	Pathogenic
35	30	M		Secondary Carrier	NAGA	NM_000262.2		chr22:g.42457056C>T	c.973G>A	p.Glu325Lys	Likely Pathogenic
36	74	M	Polyneuropathy, unspecified G62.9 Essential Tremor G25.0 Malignant Neoplasm of Prostate C61 Unspecified Sensorineural Hearing Loss H90.5 Other Seborrheic Keratosis L82.1	Primary	COL11A2	NM_080679.2		chr6:g.33141822C>T	c.2174G>A	p.Gly725Glu	VUS
				Primary	SPTLC2	NM_004863.3		chr14:g.78045365A>G	c.415T>C	p.Cys139Arg	VUS
				Secondary Carrier	SERPINA1	NM_000295.4		chr14:g.94844947C>T	c.1096G>A	p.Glu366Lys	Pathogenic
				Secondary Carrier	CEP104	NM_014704.3		chr1:g.3750458delG	c.1627delC	p.Arg543AlafsTer33	Likely Pathogenic
37	68	F	Malignant Neoplasm Of Unspecified Site Of Left Female Breast C50.912 Transient Cerebral Ischemic Attack, Unspecified G45.9 Supraventricular Tachycardia I47.1 Mild Persistent Asthma, Uncomplicated J45.30 Unspecified Osteoarthritis, Unspecified Site M19.90 Gastro‐Esophageal Reflux Disease Without Esophagitis K21.9 Essential (primary) Hypertension I10 Raynaud's Syndrome Without Gangrene I73.00 Rosacea, Unspecified L71.9 Acquired Absence Of Other Specified Parts Of Digestive Tract Z90.49 Dvrtclos Of Lg Int W/o Perforation Or Abscess W/o Bleeding K57.30	Primary	COL6A3	NM_004369.3		chr2:g.238243533C>G	c.8966‐1G>C	NA	Pathogenic
37	68	F		Secondary Carrier	ACADM	NM_000016.5		chr1:g.76226846A>G	c.985A>G	p.Lys329Glu	Pathogenic
38	63	M	Headache R51 Hyperlipidemia, Unspecified E78.5 VentricularPrematureDepolarization!49.3 Other Specified Anxiety Disorders F41.8 GERD K21.0 Gout, Unspecified M10.9 Mycosis Fungoides, Unspecified Site C84.00 Obstructive Sleep Apnea G47.33 Type 2 DM without Complications E11.9 Osteoarthritis M19.90	Primary	TET2	NM_001127208.2		chr4:g.106182914A>C	c.3955‐2A>C	NA	Likely Pathogenic
				Secondary Carrier	GJB2	NM_004004.5		chr13:g.20763744T>G	c.−22‐2A>C	NA	Pathogenic
				Secondary Carrier	PKLR	NM_000298.5		chr1:g.155261709G>A	c.517G>A	p.Asp173Asn	Pathogenic
				Secondary Carrier	SLC6A19	NM_001003841.2		chr5:g.1212453G>A	c.517G>A	p.Asp173Asn	Pathogenic
				Secondary Carrier	USH2A	NM_007123.5		chr1:g.216595590A>T	c.89T>A	p.Leu30Ter	Likely Pathogenic
39	62	F	Fibromyalgia M79.7 Primary Hypertension I10 Hyperlipidemia E78.5 Unspecified Osteoarthritis M19.90 GERD K21.0	Secondary Carrier	COL18A1	NM_030582.3		chr21:g.46911182_46911183insC	c.2651insC	p.Gly887ArgfsTer23	Pathogenic
				Secondary Carrier	VWF	NM_000552.4		chr12:g.6143978C>T	c.2561G>A	p.Arg854Gln	Pathogenic
				Secondary Disease	WNT10A	NM_025216.2		chr2:g.219755011T>A	c.682T>A	p.Phe228Ile	Likely Pathogenic
40	89	F	Idiopathic Pulmonary Fibrosis J84.112 Hyperlipidemia E78.5 Unspecified Osteoarthritis M19.90 Age‐Related Cataract H25.9	Secondary Carrier	ATP7B	NM_000053.3		chr13:g.52518281G>T	c.3207C>A	p.His1069Gln	Pathogenic
				Secondary Carrier	GJB2	NM_004004.5		chr13:g.20763744T>G	c.−22‐2A>C	NA	Pathogenic
				Secondary Carrier	PKLR	NM_001003841.2		chr1:g.155261709G>A	c.517G>A	p.Arg486Trp	Pathogenic
				Secondary Carrier	SLC6A19	NM_001003841.2		chr5:g.1212453G>A	c.517G>A	p.Asp173Asn	Pathogenic
				Secondary Carrier	USH2A	NM_007123.5		chr1:g.216595590A>T	c.89T>A	p.Leu30Ter	Likely Pathogenic
41	34	M	Rhabdomyolysis M62.82 Hemochromatosis E83.119 Abnormal Levels of Other Serum Enzymes R74.8 Pure Hypercholesterolemia E78.00	Primary	ANO5	NM_213599.2		chr11:g.22242646_22242647insA	c.184insA	p.Asn64LysfsTer15	Pathogenic
				Primary	HFE	NM_000410.3		chr6:g.26093141G>A	c.845G>A	p.Cys282Tyr	Pathogenic
				Secondary Carrier	IDUA	NM_000203.4		chr4:g.981646C>T	c.208C>T	p.Gln70Ter	Pathogenic
				Secondary Carrier	STARD9	NM_020759.2		chr15:g.42987963T>A	c.13169T>A	p.Leu4390Ter	Likely Pathogenic
42	88	M	Unspecified Hearing Loss H91.90 Angina Pectoris I20.9 Prediabetes R73.03 Macular Degeneration H35.30 Age‐Related Cataract H25.9 Unspecified Osteoarthritis M19.90 Family History of Carrier of Other Genetic Disease Z84.81	Primary	ABCA4	NM_000350.2		chr1:94508969G>A	c.3113C>T	p.Ala1038Val	Pathogenic
				Primary	CDH23	NM_022124.5		chr10:73491873A>G	c.3845A>G	p.Asn1282Ser	VUS
				Primary	HMCN1	NM_031935.2		chr1:186143745G>A	c.15914G>A	p.Arg5305Gln	VUS
				Primary	THAP1	NM_018105.2		chr8:42694447T>C	c.149A>G	p.Tyr50Cys	VUS
				Primary	THAP1	NM_018105.2		chr8:42694435C>G	c.161G>C	p.Cyc54Ser	VUS
				Secondary Carrier	FANCA	NM_000135.2		chr16:89816189C>T	c.3188G>A	p.Trp1063Ter	Pathogenic
				Secondary Carrier	SERPINA1	NM_0002095.4		chr14:94847262T>A	c.863A>T	p.Glu288Val	Pathogenic
43	72	M	Parkinson's Disease G20 Persistant Atril Fibrillation I48.1 Other Age‐Related Cataract H25.89	Secondary Disease	BRCA2	NM_000059.3		chr13:32913457C>G	c.4965C>G	p.Try1655Ter	Pathogenic
				Secondary Carrier	HFE	NM_000410.3		chr6:26093141G>A	c.845G>A	p.Cys282Tyr	Pathogenic
				Secondary Carrier	MCPH1	NM_024596.4		chr8:6296599_6296600insA	c.562insA	p.Asn189LysfsTer15	Pathogenic
				Secondary Disease	NLRP3	NM_004895.4		chr1:247587343G>A	c.598G>A	p.Val200Met	Pathogenic
				Secondary Carrier	GNRHR	NM_000406.2		chr4:68606400C>T	c.785G>A	p.Arg262Gln	Likely Pathogenic
44	52	M	Hyperlipidemia, Unspecified E78.5 Gout, Unspecified M10.9 Obstructive Sleep Apnea G47.33	Primary	STAP1	NM_012108		chr4:g.68424562G>A	35G>A	R12H	VUS
				Secondary Carrier	OCA2	NM_000275		chr15:g.28230247C>T	1327G>A	V443I	Pathogenic
				Secondary Carrier	ADAR	NM_015840		chr1:g.154574541G>C	577C>G	P193A	Pathogenic
				Secondary Carrier	PNPO	NM_018129		chr17:g.46019139A>T	98A>T	D33V	Pathogenic
				Pharmacogenetic	CYP2C9	NM_000771.3		chr10:96702047C>T	c.430C>T	NA	NA
				Pharmacogenetic	VKORC1	NM_024006.5		chr16:31107689‐1639G>A	c.−1639G>A	NA	NA
				Pharmacogenetic	CYP2C19	NM_000769.2		chr10:96521657‐806C>T	c.−806C>T	NA	NA
				Pharmacogenetic	CYP2D6	NM_000106.5		chr22:425338052988G>A	c.2988G>A	NA	NA
45	72	M	Rheumatoid Arthritis, Unspecified M06.9 Calculus Of Kidney N20.0 Malignant Melanoma Of Skin, Unspecified C43.9 Unspecified Age‐Related Cataract H25.9 Acute Myocardial Infarction, Unspecified I21.9	Secondary Carrier	BCHE	NM_000055.3		chr3:165548529T>C	c.293A>G	p.Asp98Gly	Pathogenic
				Secondary Carrier	FKBP14	NM_017946.3		chr7:30058726_3005 8727insG	c.362dupC	p.Glu122ArgfsTer7	Pathogenic
				Secondary Carrier	IRAK4	NM_016123.3		chr12:44176108A>G	c.942‐2A>G	NA	Pathogenic
				Secondary Carrier	LIPA	NM_000235.3		chr10:90982268C>T	c.894G>A	p.Gln298Gln	Pathogenic
				Secondary Carrier	FLG2	NM_001014342.2		chr1:152326321_152 326322insTA	c.3940_3941dupTA	p.Thr1314IlefsTer223	Likely Pathogenic
				Secondary Carrier	IL17RA	NM_014339.6		chr22:17566012_175 66013insT	c.31insT	p.Pro14AlafsTer42	Likely Pathogenic
				Secondary Carrier	PEX6	NM_000287.3		chr6:42935188C>T	c.1802G>A	p.Arg601Gln	Likely Pathogenic
46	56	F	Ulcerative (chronic) Proctitis Without Complications K51.20 Pure Hypercholesterolemia, Unspecified E78.00 Psoriasis, Unspecified L40.9 Other Specified Congenital Deformities Of Feet Q66.89	Secondary Carrier	HFE	NM_000410.3		chr6:26091179C>G	c.187C>G	p.His63Asp	Pathogenic
				Secondary Carrier	TUBGCP4	NM_014444.4		chr15:43675557_436 75558insT	c.578insT	p.Gly194TrpfsTer8	Pathogenic
				Secondary Disease	VKORC1	NM_024006.5		chr16:31105945C>A	c.106G>T	p.Asp36Tyr	Pathogenic
				Secondary Carrier	CTC1	NM_025099.5		chr17:8133261G>A	c.2959C>T	p.Arg987Trp	Likely Pathogenic
47	58	F	Endometriosis Of Pelvic Peritoneum N80.3 Crohn's Disease, Unspecified, Without Complications K50.90 Personal History Of Urinary Calculi Z87.442 Cervicalgia M54.2	Secondary Carrier	ABCA4	NM_000350.3		chr1:94008251C>T	c.5882G>A	p.Gly1961Glu	Pathogenic
				Secondary Carrier	ABCC6	NM_001171.5		chr16:16208798C>A	c.724G>T	p.Glu242Ter	Pathogenic
				Secondary Carrier	DNAH17	NM_173628.3		chr17:78552801_785 52802delTT	c.2182_2183delAA	p.Lys728AspfsTer19	Likely Pathogenic
				Secondary Carrier	GALT	NM_000155.3		chr9:34646576_3464 6579delCAGT	c.−116‐3_−116delGTCA	NA	Likely Pathogenic
48	71	M	Major Depressive Disorder, Recurrent, Mild F33.0 Gout, Unspecified M10.9 Athscl Heart Disease Of Native Coronary Artery W/o Ang Pctrs I25.10 Unspecified Atrial Flutter I48.92 Unspecified Age‐Related Cataract H25.9 Tinnitus, Bilateral H93.13	Secondary Carrier	AURKC	NM_001015878.1		chr19:57232070delC	c.145delC	p.Leu49TrpfsTer23	Pathogenic
				Secondary Disease	APC	NM_000038.6		chr5:112839514T>A	c.3920T>A	p.Ile1307Lys	Risk Variant
				Secondary Carrier	SUN5	NM_080675.4		chr20:32985140G>A	c.943C>T	p.Gln315Ter	Likely Pathogenic
49	65	F	Breast cancer C50.919 Mixed hyperlipidemia E78.2 Cortical age‐related cataract H25.013 Other disturbance of skin sensation R20.8	Secondary Carrier	DPYD	NM_000110.3		chr1:97828127G>A	c.220C>T	p.Arg74Ter	Likely Pathogenic
49	65	F		Secondary Carrier	LIPE	NM_005357.4		chr19:42402869delC	c.2705delG	p.Ser902ThrfsTer27	Likely Pathogenic
50	65	M	Type 2 Diabetes E11.9 Cortical age‐related cataract H25.013 Mixed hyperlipidemia E78.2 Palmar fascial fibromatosis M72.0 Benign paroxysmal vertigo H81.10	Primary	LPL	NM_000237.3		chr8:19956018A>G	c.953A>G	p.Asn318Ser	Pathogenic
				Secondary Carrier	BBS10	NM_024685.4		chr12:76347713_763 47714insA	c.271dupT	p.Cys91LeufsTer5	Pathogenic
				Secondary Carrier	PIGO	NM_032634.3 I		chr9:35092076_3509 2077insG	c.1810dupC	p.Arg604ProfsTer40	Pathogenic
				Secondary Carrier	ROM1	NM_000327.3		chr11:62613611_626 13612insG	c.339dupG	p.Leu114AlafsTer18	Likely Pathogenic
				Secondary Disease	WNT10A	NM_025216.3		chr2:218890289T>A	c.682T>A	p.Phe228Ile	Likely Pathogenic
51	66	F	Selective Deficiency Of Immunoglobulin A [iga] D80.2 Autoimmune Thyroiditis E06.3 Inflammatory Polyarthropathy M06.4	Secondary Carrier	GCDH	NM_000159.4		chr19:12896249G>C	c.680G>C	p.Arg227Pro	Pathogenic
				Secondary Carrier	DHTKD1	NM_018706.7		chr10:12112930G>A	c.2185G>A	p.Gly729Arg	Likely Pathogenic
				Secondary Carrier	SEC24D	NM_014822.4		chr4:118797796G>A	c.928C>T	p.Arg310Ter	Likely Pathogenic
52	77	M	Hereditary And Idiopathic Neuropathy, Unspecified G60.9	Primary	NOD2	NM_022162.2		chr16:50712015C>T	c.2104C>T	p.Arg702Trp	Risk Variant
				Secondary Carrier	GDF1	NM_001492.5		chr19:18869035G>T	c.681C>A	p.Cys227Ter	Pathogenic
				Secondary Carrier	MAN2B1	NM_000528.4		chr19:12657482G>T	c.1383C>A	p.Tyr461Ter	Pathogenic
				Secondary Disease	ASXL1	NM_015338.5		chr20:32433747C>T	c.1549C>T	p.Gln517Ter	Likely Pathogenic
				Secondary Carrier	MMP21	NM_147191.1		chr10:125767530A>T	c.1410+2T>A	NA	Likely Pathogenic

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Variant classification in the table reflects the classification at the time of analysis and reporting. These classifications may have changed since the analysis and reporting of these genomes to participants.

More research is needed to explore the clinical and personal impact of elective GS, across different clinical contexts and patient populations. In an effort to understand how elective GS can be integrated into routine clinical genetics practice, we evaluated a patient population that underwent elective GS on a self‐pay basis.

2. MATERIALS AND METHODS

2.1. Ethical compliance

This study was approved by the Western Institutional Review Board (WIRB #20161118).

2.2. Clinical evaluation and testing

Study recruitment occurred at the Smith Family Clinic for Genomic Medicine (SFC) located on the campus of HudsonAlpha Institute for Biotechnology in Huntsville, AL. Individuals became patients at the clinic either through consult requests from an outside provider or via self‐referral. All patients who sought a clinic appointment specifically for elective genomic testing and were 18 years or older were eligible for this study. Additionally, a single patient who came to SFC for a diagnostic purpose (neuropathy) and decided to pursue elective genome sequencing in addition to the recommended genetic testing strategy was also eligible. All participants provided informed consent and institutional review board approval was obtained from the Western Institutional Review Board.

Prior to their in‐clinic evaluation, individuals were invited to access an online patient communication and education tool, Genome Gateway. This tool allows patients to complete preliminary questionnaires and a pedigree and to receive both general and targeted educational materials. Clinical evaluation of participants included a thorough gathering of medical and family history, review of previous medical records, and a physical exam. Participants received pre‐test genetic counseling regarding potential outcomes and result types, benefits, and limitations of testing, and considerations for testing, including the limits of current knowledge and familial and insurance implications of results.

Individuals were counseled that their results would include primary findings related to a known personal or family history of disease and could include secondary findings unrelated to a known history but still medically significant if requested. The GS laboratory reports potential secondary findings in the following categories: untreatable childhood diseases (e.g., Tay‐Sachs), treatable adult‐onset diseases (e.g., Lynch syndrome), untreatable adult‐onset diseases (e.g., Autosomal Dominant Alzheimer's Disease), carrier status for a genetic disorder, and a limited number of pharmacogenetic variants. Individuals opted into the categories of secondary results that they wished to receive.

As part of standard clinical practice, clinical whole‐genome sequencing was performed to 40X coverage by the HudsonAlpha Clinical Services Lab, LLC using the HiSeq (Illumina) or NovaSeq 6000 (Illumina) platform. Secondary analysis of FASTQ files to generate variant call file (VCF) files was performed using GATK (https://gatk.broadinstitute.org/hc/en‐us) or DRAGEN Bio‐IT platform (Illumina). The VCF file was loaded into a proprietary variant annotation software platform, Carpe Novo (Worthey, 2017) or Codicem (https://hudsonalpha.org/codicem). All primary variants were confirmed via Sanger sequencing. The majority of secondary variants and pharmacogenetic variants were confirmed via Sanger sequencing. A machine learning method developed by Holt et al. (2021) allowed confidence in the accuracy of GS data without orthogonal confirmation for certain variants.

Variants were classified using the American College of Medical Genetics (ACMG) guidelines (Richards et al., 2016). Primary findings included pathogenic variants, likely pathogenic variants and variants of uncertain significance (VUSs). Secondary findings were limited to pathogenic and likely pathogenic variants in genes associated with Mendelian disorders. Selected pharmacogenetic variants were reported from the genome analysis.

Pharmacogenetic panel testing was performed by Kailos Genetics, Inc. using the MiSeq System (Illumina), with paired end 78 bp reads, to sequence selected variants within 42 pharmacogenetic genes. Kailos Genetics’ PGxComplete™ panel was used to capture and enrich targeted regions of the genome, such that 98% of the resulting sequences were aligned to the target regions. Once sequenced, a proprietary cloud‐based analysis system performed sample demultiplexing, quality assessment, alignment to the genome, variant calling, and report generation. As this pharmacogenetic test was a clinical product and enrollment occurred over a span of >4 years, the specific genes tested and variants reported evolved over time.

Patients received their clinical results and post‐test genetic counseling via in‐person appointment or conference call with a medical geneticist and genetic counselor. Prior to results disclosure, patients were queried about any changes to their results preferences, whether they had communicated with family members about their testing process, and whether they had any insurance concerns. A copy of the results was provided to patients as well as their referring physician, if requested by the patient.

3. RESULTS

3.1. Demographics and clinical evaluation

Fifty‐two patients were eligible for the study and elected to enroll. The average age of participants was 61. There was a roughly even split between males and females, with 27 males and 25 females. Ninety‐four percent (n = 49) of participants were primarily Caucasian, while four percent (n = 2) were Asian, and two percent (n = 1) were Latino. Forty‐nine participants (94%) had at least a bachelor's degree, while 30 (58%) had an advanced degree. Common professions included physicians, lawyers, and executives.

An average of 76 minutes was spent on the pre‐test clinical evaluation and counseling (range 24–161, median 75). Participants had an average of four ICD10 codes (range 1–11). Patients in the <50 years group had two ICD10 codes on average, while those in the 51–70 years group had four, and those in the >70 years group had five. Common diagnoses included hyperlipidemia, age‐related cataract, hypertension, and mild‐moderate hearing loss. Seventeen participants (33%) reported undergoing prior genetic testing; the majority of these participants had undergone direct‐to‐consumer ancestry or health testing. Ninety percent (n = 47) of participants elected to receive all possible secondary findings, while the remaining 10% elected to receive all possible secondary results except for untreatable adult‐onset conditions.

At the time of post‐test counseling, all participants reported that they were satisfied with their current insurance coverage. None had changes in their preferences at the time of results disclosure. An average of 56 minutes was spent in post‐test counseling and results discussion (range 30–102).

3.2. Clinical genome sequencing results

Twenty‐six primary results potentially related to clinical phenotype were identified in 18 of 52 participants (four individuals received multiple findings). This included 7 pathogenic variants, 2 likely pathogenic variants, 16 variants of uncertain significance, and 1 risk allele. No participants received secondary findings indicating an increased risk to develop an untreatable disease. Eight individuals (15%) received secondary findings related to treatable disease risk, three of these findings were in genes recommended for secondary disease analysis by the ACMG (Kalia et al., 2017) (two in APC (*611731), and one in BRCA2 (*600185)). Eighty‐five percent (n = 44) had a carrier status identified for at least one autosomal recessive or X‐linked disorder (range 1–7 variants, median 2 variants). As part of the limited pharmacogenetic assessment of the genome, 16 variants were reported in five individuals. None of these variants impacted a current medication (Table 1).

3.3. GS results compared to global screening array (GSA)

When compared to the variants found on the GSA (Illumina), 53% of all reported variants are represented on the array. This includes 43% of primary findings, 55% of secondary findings, and 60% of pharmacogenetic findings.

3.4. Pharmacogenetics panel testing

Fifty‐one (98%) elective GS patients underwent a separate stand‐alone pharmacogenetics panel test. The pharmacogenetics panel test reported variants that alter drug metabolism and had the potential to impact a medication in all 51 (100%) patients. Twenty‐one individuals (40%) had pharmacogenetic variants identified by this panel with the potential to impact a current medication (Table 2).

TABLE 2.

Selected pharmacogenetic variants reported by PGx Complete.

Insight number	Age	Sex	Gene	Genotype	Consequence
1	55	F	CYP2C9	1/2	Intermediate Metabolizer
2	69	F	IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
2	69	F	COMT	Val/Met	Slightly Reduced Stimulant Response
3	51	F	CYP2C19	1/17	Rapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			CYP3A4	1/22	Reduced Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
4	32	F	IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
4	32	F	CYP2C9	2/2	Poor Metabolizer
5	63	F	IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
5	63	F	COMT	Met/Met	Reduced Stimulant Response
6	73	F	CYP2C19	1/2	Intermediate Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
7	74	M	CYP2D6	4/9	Intermediate Metabolizer
			IFNL3	rs12979860T/T	Reduced Response to Hepatitis C Treatment
			CYP2C19	1/2	Intermediate Metabolizer
			CYP3A4	1/22	Reduced Metabolizer
			COMT	Met/Met	Reduced Stimulant Response
8	59	F	CYP2C9	1/2	Intermediate Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			DPYD	*1/rs67376798A	Intermediate Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
9	81	M	CYP3A4	1/22	Reduced Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Met/Met	Reduced Stimulant Response
10	79	M	CYP2C19	1/17	Rapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			CYP2C9	1/2	Intermediate Metabolizer
			COMT	Met/Met	Reduced Stimulant Response
11	57	F	CYP2C19	2/17	Intermediate to Extensive Metabolizer
11	57	F	COMT	Val/Met	Slightly Reduced Stimulant Response
12	59	M	CYP2C19	1/2	Intermediate Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
13	57	F	CYP2C19	1/2	Intermediate Metabolizer
			CYP2C9	1/3	Intermediate Metabolizer
			F5	F5 Leiden Heterozygous	Increased Thrombophilia Risk
			COMT	Met/Met	Reduced Stimulant Response
14	53	M	CYP2C19	1/2	Intermediate Metabolizer
			CYP2C9	1/2	Intermediate Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
15	31	M	CYP2C19	1/2	Intermediate Metabolizer
			TPMT	1/3A	Intermediate Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
16	61	M	CYP2D6	1/2xN	Ultrarapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
17	34	F	CYP2C9	1/2	Intermediate Metabolizer
17	34	F	COMT	Val/Met	Slightly Reduced Stimulant Response
18	51	M	CYP2C19	17/17	Ultrarapid Metabolizer
			CYP3A4	1/22	Reduced Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
19	35	F	CYP2C19	1/2	Intermediate Metabolizer
			CYP2C9	1/3	Intermediate Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
20	49	M	CYP2C9	1/2	Intermediate Metabolizer
			IFNL3	rs12979860T/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
21	44	F	CYP2C9	1/2	Intermediate Metabolizer
21	44	F	COMT	Met/Met	Reduced Stimulant Response
22	46	M	CYP2C19	1/17	Rapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
23	63	M	CYP2D6	1xN/35A	Ultrarapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			CYP2C19	1/2	Intermediate Metabolizer
24	74	M	CYP2C19	1/17	Rapid Metabolizer
			TPMT	1/3A	Intermediate Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
25	71	F	CYP2D6	2/2xN	Ultrarapid Metabolizer
			CYP2C19	1/2	Intermediate Metabolizer
			IFNL3	rs12979860T/T	Reduced Response to Hepatitis C Treatment
			F5	F5 Leiden Heterozygous	Increased Thrombophilia Risk
			COMT	Met/Met	Reduced Stimulant Response
26	59	M	CYP2D6	9/5	Intermediate Metabolizer
			CYP2C19	1/2	Intermediate Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
27	62	M	CYP2C19	2/2	Poor Metabolizer
28	71	F	CYP2C19	1/17	Rapid Metabolizer
			IFNL3	rs12979860T/T	Reduced Response to Hepatitis C Treatment
			CYP2C9	1/2	Intermediate Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
29	70	F	CYP2C19	1/2	Intermediate Metabolizer
			IFNL3	rs12979860T/T	Reduced Response to Hepatitis C Treatment
			CYP3A4	1/22	Reduced Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
30	69	F	IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
30	69	F	COMT	Val/Met	Slightly Reduced Stimulant Response
31	61	M	CYP2C19	1/2	Intermediate Metabolizer
31	61	M	COMT	Met/Met	Reduced Stimulant Response
32	55	F	CYP2D6	4/5	Poor Metabolizer
			CYP2C9	1/2	Intermediate Metabolizer
			COMT	Met/Met	Reduced Stimulant Response
33	67	M	CYP2C19	1/17	Rapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
34	67	F	CYP2C19	1/2	Intermediate Metabolizer
			CYP2C9	1/3	Intermediate Metabolizer
			TPMT	1/3A	Intermediate Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
35	30	M	CYP2C19	1/2	Intermediate Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
36	74	M	CYP2D6	4/9	Intermediate Metabolizer
			CYP2C9	1/2	Intermediate Metabolizer
			TPMT	1/3A	Intermediate Metabolizer
			COMT	Met/Met	Reduced Stimulant Response
37	68	F	CYP2D6	4/41	Intermediate Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			CYP2C19	1/17	Rapid Metabolizer
			CYP2C9	1/2	Intermediate Metabolizer
			TPMT	1/3A	Intermediate Metabolizer
38	63	M	CYP2C19	2/17	Intermediate to Extensive Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
39	62	F	CYP2C19	1/17	Rapid Metabolizer
39	62	F	COMT	Val/Met	Slightly Reduced Stimulant Response
40	89	F	CYP2C19	1/17	Rapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
41	34	M	CYP2D6	4/5	Poor Metabolizer
			CYP2C19	1/2	Intermediate Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
42	88	M	CYP2C19	1/17	Rapid Metabolizer
42	88	M	CYP2C9	1/2	Intermediate Metabolizer
43	72	M	CYP2C19	1/17	Rapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			CYP2C9	1/3	Intermediate Metabolizer
			CYP3A4	1/22	Reduced Metabolizer
44	52	M	SEPARATE PHARMACOGENETIC TEST NOT DONE
45	72	M	CYP2C9	1/3	Intermediate Metabolizer
46	56	F	CYP2C19	1/17	Rapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			COMT	Val/Met	Slightly Reduced Stimulant Response
47	58	F	CYP2C19	1/17	Rapid Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			F5	F5 Leiden Heterozygous	Increased Thrombophilia Risk
			COMT	Val/Met	Slightly Reduced Stimulant Response
48	71	M	IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
49	65	F	CYP2C19	1/2	Intermediate Metabolizer
			VKORC1	2/2	Poor Metabolizer
			CYP3A5	1/3	Reduced Metabolizer
50	65	M	CYP2D6	1/4	Intermediate Metabolizer
			CYP3A5	3/3	Poor Metabolizer
			VKORC1	3/4	Increased Metabolizer
			SLCO1B1	1b/18	Decreased Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
51	66	F	CYP2C19	1/17	Rapid Metabolizer
			CYP3A5	3/3	Poor Metabolizer
			VKORC1	3/4	Increased Metabolizer
			SLCO1B1	1a/15	Decreased Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response
52	77	M	CYP2C19	2/17	Intermediate Metabolizer
			IFNL3	rs12979860 C/T	Reduced Response to Hepatitis C Treatment
			CYP2C9	1/11	Intermediate Metabolizer
			CYP3A5	3/3	Poor Metabolizer
			SLCO1B1	1a/18	Decreased Metabolizer
			COMT	Val/Met	Slightly Reduced Stimulant Response

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4. DISCUSSION

4.1. Primary findings

Our study found nine pathogenic or likely pathogenic variants that may explain one or more aspects of the medical history in six individuals (11.5%) who underwent elective genome sequencing. This is comparable to the results from a recently published elective genome program that found 11.5% (137/1,190) of participants had a genotype–phenotype association (Hou et al., 2020).

In four cases, primary findings included a single pathogenic or likely pathogenic variant in a gene associated with autosomal recessive disease that had some overlap with the patient's history. Case 13 had follicular lymphoma and was heterozygous for a c.1582delC frameshift variant in PRF1 (*170280). Autosomal recessive PRF1‐associated hemophagocytic lymphohistiocytosis may present with lymphoma as the initial manifestation (Tesi et al., 2016). Interestingly, there is evidence that carriers of PRF1 variants are at risk for lymphomas (Chen et al., 2017; Ciambotti et al., 2014; Ding & Yang, 2013). Digenic inheritance has also been suggested (Clementi et al., 2004). Case 41 had an episode of severe rhabdomyolysis requiring an admission to the intensive care unit and was heterozygous for a c.191dupA frameshift variant in ANO5 (*608662). While the second variant in trans was not identified, the patient's phenotype is consistent with the wide variability seen in ANO5 muscle disease (Jarmula et al., 2019; Penttilä et al., 2012; Savarese et al., 2016). Reports suggest that carriers of ANO5 variants may have a mild phenotype including cramps and increased CK (Jarmula et al., 2019; Savarese et al., 2016). Case 37 had episodic facial dystonia and was heterozygous for a c.8966‐1G>C canonical splice site variant in COL6A3 (*120250). The patient's phenotype resembles cases of autosomal recessive dystonia‐27 (DYT‐27), which is characterized by a slowly progressive phenotype that starts in the hand or neck and spares the lower extremities with a median age at onset of 22 years with a range of 6–61 years (Panda & Sharawat, 2020). The variant reported in case 37 was seen in two DYT‐27 pedigrees (Jochim et al., 2016; Zech et al., 2015). Case 42 had age‐related macular degeneration (AMD) and an established pathogenic ABCA4 (*601691) variant c.3113C>T (p. Ala1038Val). ABCA4‐associated disease is a recessive disorder that ranges from early onset, rapidly progressing cone‐rod dystrophy and retinitis pigmentosa to a very late‐onset mild disease resembling AMD (Cremers et al., 2020; Zernant et al., 2017). In these cases, there are three potential explanations: (1) a second disease‐causing variant is actually present but was not detected; (2) a heterozygous state may be associated with a phenotype; and (3) these individuals have diseases that are phenocopies of the genetic disorder that they carry. These findings suggest that assessing GS in light of a patient's phenotype may prove useful, arguing that laboratories carrying out elective GS should obtain phenotypic information as we move to comprehensive elective testing(Lu et al., 2019). Individuals who do not have a standard indication for genetic testing may nevertheless have variants resulting in phenotypes related to their medical history.

In 11 cases, 17 VUSs were identified (Table 1). In the case series by Hou et al. (2020), among 42 cases, 44 VUSs were identified. Additional counseling time is required to explain these findings, follow‐up testing may incur additional expense, and reassessment of VUSs in the future may be required. VUSs are common in genomic testing (Ziats et al., 2020) and functional assays to assign these variants to the pathogenic or benign category are just beginning to appear (Almeida et al., 2020; Boonen et al., 2019; Drost et al., 2020). As a result, resolution may not be possible currently for many VUSs. Nevertheless, some VUSs can be resolved and are worth pursuing. In case 36, for example, a VUS was found in SPTLC2 (*605713), a gene associated with a treatable disorder (Fridman et al., 2019). Subsequent biochemical testing concluded that the patient did not have this condition, so the uncertainty about this result was resolved. While many VUSs are likely to be reclassified over time as benign, others will eventually prove to be disease‐causing, explaining the patient's phenotype. The opportunity to perform VUS resolution via biochemical testing, imaging, family testing, etc. requires the identification of a VUS in the first place. The identification of VUSs in elective GS relies on thorough phenotyping on the part of the ordering clinician. Importantly, careful phenotyping may identify an aspect of the individual's history or examination where an alternative diagnostic test may be superior to GS.

4.2. Clonal hematopoiesis of indeterminate potential

Case 38 (age 63) and case 52 (age 77) showed evidence of clonal hematopoiesis of indeterminate potential (CHIP) based on likely pathogenic findings in TET2 (*612839) and ASXL1 (*612990), respectively. In both cases, the pathogenic variant allele frequency (VAF) was greater than 10%. CHIP is found in approximately 7–10% of individuals over age 65 and is associated with increased cardiovascular disease due to accelerated atherogenesis and a 0.5% to 1% per year risk of developing a hematologic malignancy (Pinese et al., 2020). Most CHIP‐associated pathogenic variants occurred in three epigenetic regulators, DNMT3A *(602769), TET2, and ASXL1. VAF >10% has a higher risk of cardiovascular disease, indicating that clone size may be correlated with risk (Evans et al., 2020; Fujino & Kitamura, 2020; Karner et al., 2019; Steensma, 2018). In case 38, the patient had a subsequent myocardial event and stent placement.

4.3. Secondary disease risk

Nine variants that may affect an individual's phenotype in the future were found in eight patients. As seen in Table A1, the percentage of cases harboring an actionable secondary variant varies across studies. This reflects each study's inclusion criteria for this class of variants. In four studies, the authors include pathogenic and in some, likely pathogenic variants expected to be highly penetrant in restricted (Dewey et al., 2016; Natarajan et al., 2016; Van Hout et al., 2020) and unrestricted (Johnston et al., 2016) sets of genes. A more recent study reported secondary variants in 5.8% of cases (Hou et al., 2020). This study included pathogenic and likely pathogenic variants with a wider range of penetrance. Our study included the entire range of variant penetrance as outlined by the ClinGen Low Penetrance/Risk Allele Working Group by including low‐, moderate‐ and high‐penetrance variants. All but one of the secondary variants in our cohort would be classified as low or reduced penetrance (ClinGen, xxxx). Case 43 had the only highly penetrant variant, in BRCA2. Cases 33 and 48 had the APC Ile1307Lys representing an example of a low‐penetrance variant. Importantly, certain low‐penetrance variants like APC Ile1307Lys have established care guidelines (Gupta et al., 2017). Other low‐ or moderate‐penetrance results included variants in NLRP3 (*606416), WNT10A (*606268), NOD2 (*605956), APOC3 (*107720), and LPL (*609708). Until guidelines defining risk cutoffs (odds ratios) for low, moderate, and high penetrance are established, inconsistency in secondary variant reporting will remain.

4.4. Carrier status

All cases requested carrier status for autosomal recessive or X‐linked disorders. Eighty‐five percent (44/52) were found to be carriers of disorders that were not related to their phenotype (secondary findings). These 44 individuals were carriers of between 1 and 7 variants (median 2 variants) in 89 genes. We examined a widely available microarray, the Illumina Global Screening Array, a platform that queries variants found in ClinVar. Only 53% of the carrier variants found by GS were represented on the array. As the cost of GS testing falls, couples planning a pregnancy will be able to take advantage of more inclusive screening. Efforts in this direction are underway (Kirk et al., 2019). GS also provides an opportunity for cascade testing of other family members. In our study, many of the participants had children of reproductive age. Laboratories often report both pathogenic and likely pathogenic variants when assessing GS for carrier status. It is unclear whether a likely pathogenic variant should be reported due to the problem of the positive predictive value of such variants in rare disorders (Hagenkord et al., 2020).

4.5. Pharmacogenetic findings

We obtained pharmacogenetic data from both a stand‐alone panel of pharmacogenetic variants and from GS. Some pharmacogenetic variants identified by GS were not included in the pharmacogenetic test; these included variants in VKORC1 (*608547), DPYD (*612779), and NUDT15 (*615792). Case 15 demonstrates the utility of obtaining pharmacogenetic information through GS; in this case, the patient was found to have heterozygous variants in TPMT (*187680) and NUDT15 that in combination would result in significant toxicity if treated with mercaptopurine or thioguanine. In 21 cases, pharmacogenetic testing was relevant to current medication, emphasizing the importance of obtaining patient history in the elective testing setting. At this time, pharmacogenetic testing via GS can be cost‐prohibitive due to the need for Sanger confirmation of variants. With the development of artificial intelligence tools that may make orthogonal confirmation unnecessary, this barrier may be removed in some cases (Holt et al., 2021).

4.6. Limitations

This study has several limitations. Our small cohort is composed of individuals who are well‐educated, generally older, and primarily Caucasian. Nevertheless, their health status was typical for individuals their age and included many common multifactorial diseases. Additionally, a reanalysis of the cases with updated clinical information would likely identify new primary and secondary variants and a reclassification of the pathogenicity of some of the VUSs (Lu et al., 2020). The inclusion of secondary finding variants that are not highly penetrant is also problematic. Assessing whether a variant has moderate penetrance, low penetrance, or should be designated a “risk allele” is not well established, and therefore complicates counseling for these individuals. Understanding how the participants and their physicians used the information from GS was not addressed. These limitations point to the need for longitudinal studies measuring health outcomes, benefits, and cost‐effectiveness to assess the value of elective GS.

Establishing the usefulness of elective GS is challenging because of the different measures of utility by different stakeholders. A health insurance company might look for long‐term improvement in health outcomes as an essential measure of utility. An individual with a negative result from elective GS may feel reassured that they do not have a well‐recognized untreatable genetic disorder and consider this valuable information. A range of utility measures has been proposed reflecting this conundrum (Hayeems et al., 2020). This can be appreciated by examining whether a variant is used in patient care and when it is used. This approach to utility highlights the importance of obtaining the patient's phenotype in elective GS. It should also be noted that not all pathogenic variants are medically important.

As the cost of sequencing falls and as other elective genetic tests become more widespread, we can expect the uptake of elective genetic testing, including GS, to grow dramatically. The clinical utility and personal utility of elective GS will improve with the addition of ancestry assessment, blood groups, human leukocyte antigen typing, and polygenic risk scores. Projects are underway to improve our understanding of variants with various levels of penetrance in the general population (Carlson et al., 2020; Cirulli et al., 2020; Pinese et al., 2020). Reports and online tools geared to the needs of patients and their providers will be required to make the information understandable and provide opportunities to engage with the data as the individuals’ medical needs evolve (Yu et al., 2013). With time we can expect to use elective GS across the lifespan (Ceyhan‐Birsoy et al., 2019). In addition, if the decreasing cost and increasing quality of sequencing lead to multiple rounds of GS throughout a person's lifetime, the ability to detect somatic variation such as CHIP could add additional value.

5. CONCLUSION

As the cost of GS falls, its uses in rare disease testing and now elective testing are increasing. A growing body of literature describes the value of elective testing using GS and ES. The case series described here emphasizes the importance of patient phenotype in the analysis of an elective genome, permitting the laboratory to help individuals understand medical conditions already present. The study supports the use of GS to uncover secondary findings including CHIP, disease risk, carrier status, and pharmacogenetics. As demonstrated here, elective genome sequencing allows individuals to realize the promise of personalized medicine.

CONFLICT OF INTEREST

T.M. is the Chief Scientific Officer and R.M.M. is a co‐founder of Kailos Genetics. M.C.S. is consulted for PierianDx. No other authors have conflict(s) of interest to declare.

AUTHORS’ CONTRIBUTIONS

R.M. conceived and planned the elective genome sequencing program. M.C., K.E., V.G., W.K., and D.B. evaluated and counseled patients seen in this study. M.K., M.S., and D.B. performed genome analysis. T.M. designed and performed pharmacogenetic analysis. K.O. performed chart review and collected data. M.C. and D.B. designed the study, analyzed and interpreted results, and drafted and edited the manuscript. All authors reviewed and approved the final version of the manuscript.

ETHICAL APPROVAL

Subjects provided written informed consent before participation. The study was approved by the Western Institutional Review Board (WIRB #20161118).

ACKNOWLEDGMENTS

The authors gratefully acknowledge the participants in this study, without whom this research, and the resulting information, would not have been possible.

APPENDIX A.

TABLE A1.

Elective genome and elective exome studies.

Study	Publication date	# of Subjects enrolled in the study	GS versus ES	Medical history	Family history
Chen et al. (2012)	2012	1	GS	Yes	No
Ball et al. (2012)	2012	10	GS	Yes	Yes
Gonzalez‐Garay et al. (2013)	2013	81	ES	Yes	Yes
Dewey et al. (2014)	2014	12	GS	Yes	Yes
Johnston et al. (2015)	2015	951	ES	Yes	Yes
Reuter et al. (2018)	2018	56	GS	Yes	Yes
Rego et al. (2018)	2018	70	ES	Yes	Yes
Machini et al. (2019)	2019	100	GS	Yes	Yes
Hou et al. (2020)	2020	1,190	GS	Yes	Yes
Pinese et al. (2020)	2020	2,570	GS	Yes	No
van Rooij et al. (2020)	2020	2628	ES	Yes	No

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Medical History: A medical history was obtained from each individual enrolled in the study. Family History: A family history was obtained for each individual enrolled in the study.

Abbreviation: GS, genome sequencing; ES, exome sequencing.

Cochran, M., East, K., Greve, V., Kelly, M., Kelley, W., Moore, T., Myers, R. M., Odom, K., Schroeder, M. C., & Bick, D. (2021). A study of elective genome sequencing and pharmacogenetic testing in an unselected population. Molecular Genetics & Genomic Medicine, 9, e1766. 10.1002/mgg3.1766

DATA AVAILABILITY STATEMENT

The data that supports the findings of this study are included in the tables within the manuscript.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The data that supports the findings of this study are included in the tables within the manuscript.

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PERMALINK

A study of elective genome sequencing and pharmacogenetic testing in an unselected population

Meagan Cochran

Kelly East

Veronica Greve

Melissa Kelly

Whitley Kelley

Troy Moore

Richard M Myers

Katherine Odom

Molly C Schroeder

David Bick

Abstract

Background

Methods

Results

Conclusion

1. INTRODUCTION

TABLE 1.

2. MATERIALS AND METHODS

2.1. Ethical compliance

2.2. Clinical evaluation and testing

3. RESULTS

3.1. Demographics and clinical evaluation

3.2. Clinical genome sequencing results

3.3. GS results compared to global screening array (GSA)

3.4. Pharmacogenetics panel testing

TABLE 2.

4. DISCUSSION

4.1. Primary findings

4.2. Clonal hematopoiesis of indeterminate potential

4.3. Secondary disease risk

4.4. Carrier status

4.5. Pharmacogenetic findings

4.6. Limitations

5. CONCLUSION

CONFLICT OF INTEREST

AUTHORS’ CONTRIBUTIONS

ETHICAL APPROVAL

ACKNOWLEDGMENTS

APPENDIX A.

TABLE A1.

DATA AVAILABILITY STATEMENT

REFERENCES

Associated Data

Data Availability Statement

ACTIONS

PERMALINK

RESOURCES

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