{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:09:44Z","timestamp":1772165384557,"version":"3.50.1"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"S5","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The joint sequencing of related genomes has become an important means to discover rare variants. Normal-tumor genome pairs are routinely sequenced together to find somatic mutations and their associations with different cancers. Parental and sibling genomes reveal\n                    <jats:italic>de novo<\/jats:italic>\n                    germline mutations and inheritance patterns related to Mendelian diseases.\n                  <\/jats:p>\n                  <jats:p>Acute lymphoblastic leukemia (ALL) is the most common paediatric cancer and the leading cause of cancer-related death among children. With the aim of uncovering the full spectrum of germline and somatic genetic alterations in childhood ALL genomes, we conducted whole-exome re-sequencing on a unique cohort of over 120 exomes of childhood ALL quartets, each comprising a patient's tumor and matched-normal material, and DNA from both parents. We developed a general probabilistic model for such quartet sequencing reads mapped to the reference human genome. The model is used to infer joint genotypes at homologous loci across a normal-tumor genome pair and two parental genomes.<\/jats:p>\n                  <jats:p>\n                    We describe the algorithms and data structures for genotype inference, model parameter training. We implemented the methods in an open-source software package (Q\n                    <jats:sc>UAD<\/jats:sc>\n                    GT) that uses the standard file formats of the 1000 Genomes Project. Our method's utility is illustrated on quartets from the ALL cohort.\n                  <\/jats:p>","DOI":"10.1186\/1471-2105-14-s5-s3","type":"journal-article","created":{"date-parts":[[2013,4,10]],"date-time":"2013-04-10T14:15:13Z","timestamp":1365603313000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Joint genotype inference with germline and somatic mutations"],"prefix":"10.1186","volume":"14","author":[{"given":"Eric","family":"Bareke","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Virginie","family":"Saillour","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Fran\u00e7ois","family":"Spinella","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramon","family":"Vidal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jasmine","family":"Healy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Sinnett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikl\u00f3s","family":"Cs\u0171r\u00f6s","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,4,10]]},"reference":[{"issue":"10","key":"5771_CR1","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1038\/nbt1486","volume":"26","author":"J Shendure","year":"2008","unstructured":"Shendure J, Li H: Next-generation DNA sequencing. 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