Patients who were referred with positive clinical CH determination found to be CH− on CHIVEseq assay
| Study ID . | Clinically identified mutation(s) . | Clinical panel . | Reason(s) . |
|---|---|---|---|
| 0006 | JAK2 p.V617F (VAF 0.2%) | Tempus (liquid biopsy) | Below 2% VAF threshold |
| 1020 | TET2 p.A915P (VAF 45%) | Myeloid neoplasm NGS Panel | Germ line mutation; mutation is outside of TET2 catalytic domain & therefore not considered a CH variant by CHIVEseq |
| 1071 | BCOR p.E1081K (VAF > 99%) | Myeloid neoplasm NGS panel | Germ line mutation; BCOR gene not covered on CHIVEseq assay |
| 1085 | CUX1 p.P1080∗ (VAF 5.18%) | Myeloid neoplasm NGS panel | CUX1 gene not covered on CHIVEseq assay |
| 1095 | JAK2 p.N691H (VAF 47.87%) | Myeloid neoplasm NGS panel | Germ line mutation; mutation not considered a CH variant on CHIVEseq assay |
| 1103 | TET2 p.C88R (VAF 45.94%) CSF3R p.R698C (VAF 48.92%) | Myeloid neoplasm NGS panel | TET2: germ line mutation; mutation is outside of TET2 catalytic domain and therefore not considered a CH variant by CHIVEseq CSF3R: germ line mutation; CSF3R gene not covered on CHIVEseq assay |
| 2001 | BCORL p.V881E (VAF 49.52%) | Myeloid neoplasm NGS panel | Germ line mutation; BCORL gene not covered on CHIVEseq assay |
| 2006 | SH2B3 p.L429V (VAF 48.58%) | Myeloid neoplasm NGS panel | Germ line mutation; SH2B3 gene not covered on CHIVEseq assay |
| 2011 | CALR p.E381del (VAF 48.97%) BCOR p.S209L (VAF 99.2%) | Myeloid neoplasm NGS panel | CALR: germ line mutation; CALR gene not covered on CHIVEseq assay BCOR germ line mutation; BCOR gene not covered on CHIVEseq assay |
| 2015 | JAK2 p.I724T (VAF 48.99%) SMC1A p.I1062M (VAF 50.47%) TET2 p.A289P (VAF 48.99%) | Myeloid neoplasm NGS panel | JAK2: germ line mutation; mutation not considered a CH variant by CHIVEseq SMC1A: germ line mutation; SMC1A gene not covered on CHIVEseq assay TET2: germ line mutation; mutation is outside of TET2 catalytic domain and therefore not considered a CH variant by CHIVEseq |
| 2016 | CUX1 p.E1373Q (VAF 48.62%) CUX1 p.R843K (VAF 50.35%) | Myeloid neoplasm NGS panel | Germ line mutations; CUX1 gene not covered on CHIVEseq assay |
| 2019 | DNMT3A p.A462V (VAF 57%) | Myeloid neoplasm NGS panel | Germ line mutation |
| 2041 | SF3B1 p.K700E (VAF 3.1%) DNMT3A p.L888Q (VAF 2.1%) | NeoTYPE MDS/CMML profile | SF3B1: this site was sequenced but the SF3B1 K700E variant was not identified, including at VAF <2%. DNMT3A: mutation is not considered CH by conventional definitions |
| 2046 | SH2B3 p.S213R (VAF 47.77%) | Myeloid neoplasm NGS panel | Germ line mutation; SH2B3 gene not covered on CHIVEseq assay |
| 2059 | KDM6A p.R621H (VAF 51%) | Advanced NGS myeloid report | Germ line mutation; KDM6A gene not covered on CHIVEseq assay |
| 2068 | ASXL1 p.G646Wfs∗12 (10%) | Advanced NGS myeloid report | Commonly encountered artifact in a homopolymer region of the CHIVEseq assay. Our practice is to categorize these variants as CH when VAF is > 10%. This variant was not considered CH because the VAF was 6%. |
| Study ID . | Clinically identified mutation(s) . | Clinical panel . | Reason(s) . |
|---|---|---|---|
| 0006 | JAK2 p.V617F (VAF 0.2%) | Tempus (liquid biopsy) | Below 2% VAF threshold |
| 1020 | TET2 p.A915P (VAF 45%) | Myeloid neoplasm NGS Panel | Germ line mutation; mutation is outside of TET2 catalytic domain & therefore not considered a CH variant by CHIVEseq |
| 1071 | BCOR p.E1081K (VAF > 99%) | Myeloid neoplasm NGS panel | Germ line mutation; BCOR gene not covered on CHIVEseq assay |
| 1085 | CUX1 p.P1080∗ (VAF 5.18%) | Myeloid neoplasm NGS panel | CUX1 gene not covered on CHIVEseq assay |
| 1095 | JAK2 p.N691H (VAF 47.87%) | Myeloid neoplasm NGS panel | Germ line mutation; mutation not considered a CH variant on CHIVEseq assay |
| 1103 | TET2 p.C88R (VAF 45.94%) CSF3R p.R698C (VAF 48.92%) | Myeloid neoplasm NGS panel | TET2: germ line mutation; mutation is outside of TET2 catalytic domain and therefore not considered a CH variant by CHIVEseq CSF3R: germ line mutation; CSF3R gene not covered on CHIVEseq assay |
| 2001 | BCORL p.V881E (VAF 49.52%) | Myeloid neoplasm NGS panel | Germ line mutation; BCORL gene not covered on CHIVEseq assay |
| 2006 | SH2B3 p.L429V (VAF 48.58%) | Myeloid neoplasm NGS panel | Germ line mutation; SH2B3 gene not covered on CHIVEseq assay |
| 2011 | CALR p.E381del (VAF 48.97%) BCOR p.S209L (VAF 99.2%) | Myeloid neoplasm NGS panel | CALR: germ line mutation; CALR gene not covered on CHIVEseq assay BCOR germ line mutation; BCOR gene not covered on CHIVEseq assay |
| 2015 | JAK2 p.I724T (VAF 48.99%) SMC1A p.I1062M (VAF 50.47%) TET2 p.A289P (VAF 48.99%) | Myeloid neoplasm NGS panel | JAK2: germ line mutation; mutation not considered a CH variant by CHIVEseq SMC1A: germ line mutation; SMC1A gene not covered on CHIVEseq assay TET2: germ line mutation; mutation is outside of TET2 catalytic domain and therefore not considered a CH variant by CHIVEseq |
| 2016 | CUX1 p.E1373Q (VAF 48.62%) CUX1 p.R843K (VAF 50.35%) | Myeloid neoplasm NGS panel | Germ line mutations; CUX1 gene not covered on CHIVEseq assay |
| 2019 | DNMT3A p.A462V (VAF 57%) | Myeloid neoplasm NGS panel | Germ line mutation |
| 2041 | SF3B1 p.K700E (VAF 3.1%) DNMT3A p.L888Q (VAF 2.1%) | NeoTYPE MDS/CMML profile | SF3B1: this site was sequenced but the SF3B1 K700E variant was not identified, including at VAF <2%. DNMT3A: mutation is not considered CH by conventional definitions |
| 2046 | SH2B3 p.S213R (VAF 47.77%) | Myeloid neoplasm NGS panel | Germ line mutation; SH2B3 gene not covered on CHIVEseq assay |
| 2059 | KDM6A p.R621H (VAF 51%) | Advanced NGS myeloid report | Germ line mutation; KDM6A gene not covered on CHIVEseq assay |
| 2068 | ASXL1 p.G646Wfs∗12 (10%) | Advanced NGS myeloid report | Commonly encountered artifact in a homopolymer region of the CHIVEseq assay. Our practice is to categorize these variants as CH when VAF is > 10%. This variant was not considered CH because the VAF was 6%. |
Mutation in question, clinical panel, and reasoning for non-CH diagnosis are reported.
BCOR, BCL6 corepressor.