The poor outcomes from pancreatic cancer result from the inability to identify patients with early-stage disease. Most patients present with advanced disease and their expected 5-year survival is only 3%.1 Current imaging modalities and serum markers are insufficiently sensitive and specific in the general population to be successfully employed in early detection. As a result, many prevention strategies have focused on identifying high-risk patients through genetic susceptibility genes.
Over the last decade, several large, matched cohort studies from the Mayo Clinic, Memorial Sloan Kettering, Nanjing Medical University, and Johns Hopkins University have identified several pathogenic germline variants (PGVs) that are associated with the development of pancreatic ductal adenocarcinoma (PDAC).2–4 These include but are not limited to PGVs in BRCA2, ATM, TP53, BRCA1, APC, CDKN2A, PALB2, STK11, and the mismatch repair genes associated with Lynch Syndrome (MLH1, MSH2, MSH6, and PMS2). In 2019, these findings culminated in recommendations from the American Society of Clinical Oncology and the National Comprehensive Cancer Network that all patients with PDAC, regardless of family history or age of diagnosis, should undergo germline testing on a multi-gene panel test for PGVs in cancer susceptibility genes.5,6
To facilitate these recommendations Invitae®, a genetic testing company, initiated the Detect Hereditary Pancreatic Cancer program (DETECT) through which patients diagnosed with PDAC were offered no-charge genetic testing. The program launched on 9/5/2019 and closed on 2/15/2022. The DETECT panel was designed so participants would receive STAT BRCA1/2 panel testing first and auto-reflex to either the Invitae Common Hereditary Cancers Panel (42–47 genes) or Invitae Multi-Cancer Panel (80–84 genes) with the option to add on preliminary evidence chronic pancreatitis genes (CFTR, CASR, CTRC, CPA1, PRSS1, SPINK1). We evaluated the incidence of germline alterations in pancreatic adenocarcinoma patients enrolled in this program.
1203 PDAC participants had germline testing performed over the duration of the program. The pancreatitis panel was added to the testing of common cancer gene panels in 445 of those patients. In total, 20.4% (245/1203) were found to have PGVs and 2.2% (27/1203) had more than one PGV. The most common alterations identified included BRCA2 (2.4%), ATM (2.3%), MUTYH (1.8%), and CHEK2 (1.7%) (Table 1). Germline alterations in pancreatitis genes, CFTR, CTRC, PRSS1, or SPINK1, occurred in 14.8% (66/445) of PDAC patients who underwent testing of these genes. The majority were CFTR alterations identified in 53/445 (11.9%).
Table 1. Pathogenic germline variants in PDAC patients.
A: 1203 PDAC patients underwent expanded germline testing through the Detect Hereditary Pancreatic Cancer initiative and 20.4% were found to have PGVs. Ordering practitioners added a pancreatitis panel to 445 of the 1203 cases and CFTR pathogenic variants were prevalent and most common 53/445. The alterations are listed by prevalence (%). All variants listed are confirmed pathogenic. B: Pathogenic germline variants within CFTR found in patients with pancreatic adenocarcinoma
| A | |||
|---|---|---|---|
| CFTR | 53 (11.9%) | TP53 | 3 (0.2%) |
| BRCA2 | 29 (2.4%) | PRSS1 | 1 (0.2%) |
| ATM | 28 (2.3%) | BLM | 2 (0.2%) |
| SPINK1 | 8 (1.8%) | BARD1 | 2 (0.2%) |
| MUTYH | 21 (1.8%) | HOXB13 | 2 (0.2%) |
| CHEK2 | 20 (1.7%) | RAD50 | 2 (0.2%) |
| CTRC | 5 (1.1%) | MSH2 | 2 (0.2%) |
| NTHL1 | 9 (0.8%) | NF1 | 2 (0.2%) |
| BRIP1 | 9 (0.8%) | PMS2 | 2 (0.2%) |
| APC | 9 (0.7%) | VHL | 2 (0.2%) |
| BRCA1 | 7 (0.6%) | CDKN1C | 1 (0.1%) |
| MSH6 | 7 (0.6%) | EGFR | 1 (0.1%) |
| PALB2 | 7 (0.6%) | MITF | 1 (0.1%) |
| NBN | 6 (0.5%) | RET | 1 (0.1%) |
| WRN | 5 (0.4%) | MSH3 | 1 (0.1%) |
| CDKN2A (p16INK4a) | 5 (0.4%) | SDHB | 1 (0.1%) |
| FANCC | 4 (0.4%) | RAD51C | 1 (0.1%) |
| FH | 4 (0.3%) | CDKN2A (p14ARF) | 1 (0.1%) |
| SDHA | 4 (0.3%) | MEN1 | 1 (0.1%) |
| RECQL4 | 3 (0.3%) | MLH1 | 1 (0.1%) |
| CFTR Alteration Subtype | Other nomenclature | N (53) | Minor Allele Frequency (MAF)a |
| B | |||
| c.1210–34 TG[11]T[5] | 5T; TG11 | 24 | 0.033 (3.3% ie >1%) |
| c.1210–34 TG[12]T[5] | 5T; TG12 | 8 | <0.01 (<1%) |
| c.1210–34 TG[13]T[5] | 5T; TG13 | 1 | <0.01 (<1%) |
| NM_000492.3:c.1327G > T | p.Asp443Tyr | 1 | <0.01 (<1%) |
| NM_000492.3:c.1521_1523del | p.Phe508del; aka ΔF508 | 12 | 0.01 (1%) |
| NM_000492.3:c.1624G > T | p.Gly542 | 2 | <0.01 (<1%) |
| NM_000492.3:c.2657+5G > A | Intronic | 1 | <0.01 (<1%) |
| NM_000492.3:c.3454G > C | p.Asp1152His | 2 | <0.01 (<1%) |
| NM_000492.3:c.3846G > A | p.Trp1282 | 1 | <0.01 (<1%) |
| NM_000492.3:c.3909C > G | p.Asn1303Lys | 1 | <0.01 (<1%) |
Highest sub-population minor allele frequency as reported by gnomAD and 1000’s genome project.
Due to the unexpected prevalence of pancreatitis-associated PGVs, we compared the clinical characteristics and demographics of these patients to those with other PGVs versus those without any PGVs (Table 2). There were no clinically significant differences between the 3 groups for clinician-reported stage, clinician-reported ancestry, or family history. The median age at testing for PDAC patients was similar across the groups. There was a trend toward male predominance in those with PGVs in a common hereditary cancer gene, however, this did not reach a statistical significance. Regarding ancestry, there were no significant differences found in patients with PGVs as compared to those without PGVs. However, most patients enrolled in the program were clinician-reported white, and Black/African American patients only accounted for 28/1203 of PDAC patients tested. Notably, there were higher PGV yields in those with family history of cancer, across groups, ranging from 85 to 90%.
Table 2. PDAC subjects with pathogenic germline variants (PGVs) in pancreatitis genes as compared to other germline variants.
A significant number of PDAC patients were identified with PGVs in pancreatitis genes. Demographic data, self-reported family history, and staging information was evaluated among those with pancreatitis associated PGVS (Pancreatitis), non-pancreatitis associated PGVS (Germline) and compared both groups to those without any PGVs (Neither)
| Age at testing | 0.5086 | 0.1234 | |||
| N | 66 | 186 | 950 | ||
| Mean (SD) | 67.2 (10.8) | 65.0 (10.9) | 66.3 (10.3) | ||
| Range | (40.0–83.0) | (32.0–85.0) | (19.0 – 89.0) | ||
| Sex | 0.3445 | 0.0334 | |||
| Female | 28 (42.4%) | 76 (40.0%) | 464 (48.4%) | ||
| Male | 38 (57.6%) | 114 (60.0%) | 494 (51.6%) | ||
| Clinician-reported ancestry | 0.3500 | 0.2118 | |||
| Missing | 10 | 16 | 75 | ||
| Asian | 1 (1.8%) | 3 (1.7%) | 47 (5.3%) | ||
| Black/African-American | 1 (1.8%) | 5 (2.9%) | 22 (2.5%) | ||
| Hispanic | 2 (3.6%) | 9 (5.2%) | 30 (3.4%) | ||
| Jewish | 3 (5.4%) | 10 (5.7%) | 32 (3.6%) | ||
| Other | 2 (3.6%) | 17 (9.8%) | 96 (10.9%) | ||
| White/Caucasian | 47 (83.9%) | 130 (74.7%) | 656 (74.3%) | ||
| Family History | 0.7502 | 0.9705 | |||
| Missing | 46 | 125 | 616 | ||
| no | 2 (10.0%) | 10 (15.4%) | 52 (15.2%) | ||
| yes | 18 (90.0%) | 55 (84.6%) | 290 (84.8%) | ||
| Cancer Stage | 0.7813 | 0.9503 | |||
| Missing | 50 | 130 | 640 | ||
| 0/1A/1B | 2 (12.5%) | 8 (13.3%) | 37 (11.6%) | ||
| IIA/IIB | 1 (6.3%) | 10 (16.7%) | 50 (15.7%) | ||
| III | 2 (12.5%) | 11 (18.3%) | 54 (17.0%) | ||
| IV | 11 (68.8%) | 31 (51.7%) | 177 (55.7%) |
Of the 53 patients with pathogenic monoallelic CFTR alterations, 10 distinct variants were identified (Table 1b). All the variants identified can be cystic fibrosis (CF) causing (when either homozygous or compound heterozygous with another PGV) and have been associated with a variable prevalence of pancreatic insufficiency. Most of these variants are exceedingly rare in the general population as 8/10 CFTR variants had a minor allele frequency (MAF) of less than 1%, even among sub-populations with the highest MAF. The 5T; TG11 variant has a MAF of 3.3%, and the c.1521_1523del PV has a MAF of 1% among Europeans as reported by gnomAD and 1000’s genome project.
Of interest are the TG track mutations, Table 1b (n = 33). The T5 allele at the polymorphic Tn locus of the CFTR gene has been shown to be a disease-causing mutation with incomplete penetrance.7 Notably, T5 in combination with longer TG tract like TG12 or TG13 results in a higher proportion of mis-splicing events resulting in skipping of exon 10 (legacy exon 9).7,8 In a small study of non-CF healthy individuals, T5 with TG12 or T5 with TG13 were not found because of the rarity of these combination.9 In a large cohort of patients tested for CFTR, TG[11–13]T5 variants were significantly enriched in individuals with a high suspicion of CF.10 In addition, those with TG[11–13]T5/CFvar generally had single-organ involvement, milder symptoms, variable expressivity, and reduced penetrance. T5 in combination with TG12 (n = 8) and with TG13(n = 1) in the cohort of individuals with pancreatic cancer is of interest and merits further evaluation.
Some of the other variants found include c.1327G > T, p.Asp443Tyr; complex allele, found frequently in cis with p.Gly576Ala and p.Arg668Cys.11 This variant (p.Asp443Tyr) has varying clinical significance when present with a CF-causing variant. The variant c.1521_1523del, (p.Phe 508del), is the most common CF-causing variant, and is represented in 14 of the 56 individuals. The c.1624G > T (p.Gly542*), is a disease-causing variant, (n = 2) Similarly, c.2657+5G > A, is also a disease-causing variant, due to abnormal RNA splicing.12 c.3454G > C, p.Asp1152His has varying clinical consequences while c.3846G > A, Trp1282*, and c.3909C > G, Asn1303Lys are disease-causing variants.13
Previous studies have suggested that patients with chronic pancreatitis harboring alterations in CFTR, SPINK1, and PRSS1 will have a 2–12-fold increased risk of pancreatic cancer development.14,15 In addition, in patients with CF the risk of pancreatic and other gastrointestinal malignancies is substantial and merits special consideration including early screening.16 However, the relationships between pathogenic CFTR carrier alterations, their associated clinical presentations, and the risk of pancreatic cancer are unclear and deserve additional study.
This effort to democratize germline testing in pancreatic cancer patients reinforces the clinical relevance of expanded germline multi-gene panel testing. PGVs are frequent and there are a surprising number of pancreatitis associated PGVs in patients with PDAC. Further study is needed to better understand the risk and mechanism of PDAC development in carriers, and further develop screening strategies. Unfortunately, this real-world program also demonstrates that efforts to be inclusive of all patients, even by eliminating financial barriers, are still often unsuccessful in reaching those from underserved communities. As such the PGV landscape in black/African American patients with PDAC requires additional outreach and study.
Key Points.
Question -
What is the prevalence of cancer and pancreatitis-associated pathogenic germline variants (PGVs) in PDAC patients enrolled in an expanded panel multi-gene panel testing program?
Findings -
Of the 1203 PDAC participants enrolled in the Invitae® Hereditary Detect Program, 20.4% of subjects were found to have pathogenic germline variants (PGVs) in common hereditary cancer genes. Germline alterations in pancreatitis genes, CFTR, CTRC, PRSS1, or SPINK1, occurred in 14.8% (66/445) of PDAC patients who underwent testing of these genes. The majority were CFTR alterations identified in 53/445 (11.9%).
Meaning -
Pancreatitis-associated PGVs and specifically CFTR are high in PDAC patients and their inclusion in expanded panels are recommended.
Contributor Information
Andrew Hendifar, Samuel Oschin Comprehensive Cancer Center, Cedars Sinai Medical Center, Los Angeles CA, USA.
Megan Hitchins, Samuel Oschin Comprehensive Cancer Center, Cedars Sinai Medical Center, Los Angeles CA, USA.
Marie Lauzon, Samuel Oschin Comprehensive Cancer Center, Cedars Sinai Medical Center, Los Angeles CA, USA.
Kathryn E. Hatchell, Invitae, San Francisco, CA, USA
Brandie Heald, Invitae, San Francisco, CA, USA.
Stephen Pandol, Cedars Sinai, Medicine, USA.
Anjaparavanda P. Naren, Cedars Sinai, Medicine, USA
Arsen Osipov, Samuel Oschin Comprehensive Cancer Center, Cedars Sinai Medical Center, Los Angeles CA, USA.
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