Table 1 Details on the 11 samples where Gauchian and Sanger are inconsistent
From: Reply to: Is Gauchian genotyping of GBA1 variants reliable?
Gauchian calls | Sanger Assessment, Tayebi et al. | Our assessment | ||||
|---|---|---|---|---|---|---|
Sample | Copy Number of GBA1 and GBAP1 | GBAP1-like variant in exons 9–11 | Other unphased variants | Genotype | Prediction | |
Pat_08 | 4 | None | p.Asn409Ser | p.Asn409Ser/p.Gln389Ter | False Negative | Missed variant Gln389Ter is not on Gauchian’s target list |
Pat_28 | 4 | None | p.Arg535His | p.Arg535His/Cys381Tyr | False Negative | Missed variant Cys381Tyr is not on Gauchian’s target list |
Pat_58 | 4 | None | p.Asn409Ser, p.Arg296Ter | p.Asn409Ser, p.Arg296Ter, c.203delC | False Negative | Missed variant c.203delC is not on Gauchian’s target list |
Pat_26 | 4 | None | p.Asn409Ser | p.Asn409Ser/p.Arg502Cys | False Negative | Missed variant Arg502Cys (should be Arg502His) is not on Gauchian’s target list. Tayebi et al.’s Supplementary Fig. 1 shows no variant at p.Arg502Cys (c.1504 C > T), but a different variant at the neighboring position, p.Arg502His (c.1505 G > A), which is not on Gauchian’s target list. |
Pat_75 | None (No Call) | NA | NA | p.Arg502Cys/p.Arg159Trp | Missed | Copy number is a no-call due to high variation in depth so no further variant calling was performed. Coverage MAD 0.269 |
Pat_76 | None (No Call) | NA | NA | p.Asn409Ser/p.Asn409Ser | Missed | Copy number is a no-call due to high variation in depth so no further variant calling was performed. Coverage MAD 0.128 |
Pat_79 | None (No Call) | NA | NA | p.Leu483Pro/p.Arg502Cys | Missed | Copy number is a no-call due to high variation in depth so no further variant calling was performed. Coverage MAD 0.127 |
Pat_03 | 4 | None | p.Asn409Ser | p.Asn409Ser/p.Asn409Ser | False Negative | Gauchian call is supported by reads, see Tayebi et al.’s Supplementary Fig. 1. |
Pat_47 | 4 | None | p.Asn409Ser | p.Asn409Ser/p.Leu483Pro | False Negative | True false negative |
Pat_16 | 3 | c.1263del+RecTL/ | p.Asn409Ser, p.Asn409Ser | p.Asn409Ser, c.1263del+RecTL | False Positive | Heterozygous p.Asn409Ser misgenotyped as homozygous as Gauchian did not know the exact breakpoint of the c.1263del+RecTL deletion, which is very close to p.Asn409Ser. |
Pat_92 | 7 | p.Asp448His/p.Leu483Pro,p.Asp448His | p.Asp448His/ p.Leu483Pro+Rec7 | False Negative | There is no false negative. Rec7 is reflected in the copy number call (copy number gain). This GBAP1 duplication does not have any functional impact on GBA1, so Gauchian does not report it as a GBA1 variant. Heterozygous p.Asp448His misgenotyped as homozygous. | |
