PMC:6037202 / 18093-19392 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":"To compare detection rates of loss-of-function variants in our cohort with a large-scale WGS dataset unselected for neoplastic phenotypes, we interrogated gnomAD18 (data downloaded in February 2018) for variants occurring in the same set of 83 genes. Only truncating or splice-site variants were considered for comparison purposes because these are less likely to be false positives and made up 52/63 (82.5%) (see Results) of the P/LP variants in our cohort. Variants extracted from gnomAD were filtered and assessed in the same manner as those occurring in the MPT cohort. The frequency of variants assessed as P/LP was also calculated for males and females, and the sex distribution of individuals in the gnomAD dataset (55.3% male and 44.6% female) was estimated with mean allele count across all positions in the gnomAD VCF file of chromosomes 1–22. In order to estimate gnomAD P/LP variant frequency as though the sex distribution was equivalent to that in the MPT series (23% male and 77% female), we applied the sex-specific frequency to the estimated total number of gnomAD females (n = 6,929) and a reduced number of males (n = 2,064) that would achieve the desired proportion. We then summed the respective allele-frequency estimates to provide a figure for comparison with the MPT series.","tracks":[{"project":"2_test","denotations":[{"id":"29909963-27535533-2051616","span":{"begin":161,"end":163},"obj":"27535533"}],"attributes":[{"subj":"29909963-27535533-2051616","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#bfec93","default":true}]}]}}