PMC:6037202 / 31198-33043 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/6037202","sourcedb":"PMC","sourceid":"6037202","source_url":"https://www.ncbi.nlm.nih.gov/pmc/6037202","text":"Coverage and Comparison with Panel\nMean depth in WGS data of coding bases in the 83 genes analyzed was 35× (SD = 7.5), and 100% were covered at ≥10×. Coverage was also considered for 68 of the genes also sequenced by the TCP. In WGS data, 100% of target bases were covered at ≥10×, and the mean depth was 35.3 (SD = 7.4). Coverage analysis pertaining to those 68 genes from the 411 (89.3%) participants also undergoing sequencing with the TCP showed 99.1% target bases at ≥10× and a mean depth of 807.3 (SD = 793.2).\nA comparison of the variant detection was performed on the basis of the 105 ACMG-assessed SNVs and indels that were detected by WGS and were within a gene sequenced by the TCP. 99/105 variants were called from TCP data with quality indicators sufficient to pass filters used for the WGS data. Five undetected variants—including one P/LP PMS2 variant (c.741−742insTGAAG [p.Pro247_Ser248fs] [Ensembl: ENST00000265849; GenBank: NM_000535.6]), where 58/202 (20.6%) reads contained the insertion—were indels for which IGV review showed a VAF below the threshold for filtering. One undetected variant in TMEM127 (MIM: 613403) (c.665C\u003eT [p.Ala222Val] [Ensembl: ENST00000258439; GenBank: NM_017849.3]) was covered by only two reads.\nThe filtering and assessment process applied to WGS data was also used for variants called from TCP data generated from the same 411 individuals. 108/110 TCP variants that passed filters and went forward for ACMG assessment were also called from WGS data, meaning that two variants (assessed as pathogenic) were not detected by WGS. This was because the VAF was marginally below the filtering threshold of 33% for ATM (c.2426C\u003eA [p.Ser809∗] [Ensembl: ENST00000278616; GenBank: NM_000051]) (7/22 [32%] reads) and MAX (c.97C\u003eT [p.Arg33∗] [Ensembl: ENST00000358664; GenBank: NM_002382]) (9/29 [31%] reads).","divisions":[{"label":"title","span":{"begin":0,"end":34}},{"label":"p","span":{"begin":35,"end":516}},{"label":"p","span":{"begin":517,"end":1241}}],"tracks":[]}