Table 2.

Overview of false negative samples. Variants not detected after applying the less strict extra VUS filter strategy are listed. tNGS: targeted NGS; WES: whole-exome sequencing; WGS: whole-genome sequencing; hom.: homozygous; AR: autosomal recessive; XL: recessive X-linked; VUS: variant of unknown significance.

tNGS			WES			WGS
Sample	Variant (s)	Reason Variant Missed	Sample	Variant (s)	Reason Variant Missed	Sample	Variant (s)	Reason Variant Missed
			6	SLC22A5 Chr5(GRCh37):g.131705516G>A NM_003060.4:c.-149G>A p.?; heterozygous	3′UTR variant filtered out, but present in raw data/other variant VUS	6	SLC22A5 Chr5(GRCh37):g.131705516G>A NM_003060.4:c.-149G>A p.?; heterozygous	3′UTR variant filtered out, but present in raw data/other variant VUS
30	ETFA Chr15(GRCh37):g.76603769C>T NM_000126.4:c.-40G>A p.?: homozygous	hom. VUS/present in raw data	30	ETFA Chr15(GRCh37):g.76603769C>T NM_000126.4:c.-40G>A p.?: homozygous	hom. VUS/present in raw data	30	ETFA Chr15(GRCh37):g.76603769C>T NM_000126.4:c.-40G>A p.?: homozygous	hom. VUS/present in raw data
34	BCKDHA Chr19(GRCh37):g.41916527T>A NM_000709.4:c.109-15T>A p.?; homozygous	hom. VUS/present in raw data	34	BCKDHA Chr19(GRCh37):g.41916527T>A NM_000709.4:c.109-15T>A p.?; homozygous	hom. VUS/present in raw data	34	BCKDHA Chr19(GRCh37):g.41916527T>A NM_000709.4:c.109-15T>A p.?; homozygous	hom. VUS/present in raw data
36	CAD Chr2(GRCh37):g.27460617C>T NM_004341.5:c.4595C>T p.(Ala1532Val); homozygous	hom. VUS/present in raw data	36	CAD Chr2(GRCh37):g.27460617C>T NM_004341.5:c.4595C>T p.(Ala1532Val); homozygous	hom. VUS/present in raw data	36	CAD Chr2(GRCh37):g.27460617C>T NM_004341.5:c.4595C>T p.(Ala1532Val); homozygous	hom. VUS/present in raw data
39	FOLR1 Chr11(GRCh37):g.71906952T>C NM_016729.3:c.505T>C p.(Cys169Arg); homozygous	hom. VUS/present in raw data				3	CBS Chr21(GRCh37):g.44478972C>T NM_000071.3:c.1330G>A p.(Asp444Asn); heterozygous CBS Chr21(GRCh37):g.44484032_4484034del NM_000071.3:c.805_807del p.(Lys269del); heterozygous	Low coverage and pseudogene
						31	ABCD1 ChrX(GRCh37):g.152991164A>G NM_000033.4:c.443A>G p.(Asn148Ser); hem.	Low coverage and pseudogene