ContEst: estimating cross-contamination of human samples in next-generation sequencing data - PubMed (original) (raw)

The Proteogenomics of Prostate Cancer Radioresistance.

Haas R, Frame G, Khan S, Neilsen BK, Hong BH, Yeo CPX, Yamaguchi TN, Ong EHW, Zhao W, Carlin B, Yeo ELL, Tan KM, Bugh YZ, Zhu C, Hugh-White R, Livingstone J, Poon DJJ, Chu PL, Patel Y, Tao S, Ignatchenko V, Kurganovs NJ, Higgins GS, Downes MR, Loblaw A, Vesprini D, Kishan AU, Chua MLK, Kislinger T, Boutros PC, Liu SK. Haas R, et al. Cancer Res Commun. 2024 Sep 1;4(9):2463-2479. doi: 10.1158/2767-9764.CRC-24-0292. Cancer Res Commun. 2024. PMID: 39166898 Free PMC article.

Low-level brain somatic mutations in exonic regions are collectively implicated in autism with germline mutations in autism risk genes.

Kim IB, Kim MH, Jung S, Kim WK, Lee J, Ju YS, Webster MJ, Kim S, Kim JH, Kim HJ, Kim J, Kim S, Lee JH. Kim IB, et al. Exp Mol Med. 2024 Aug;56(8):1750-1762. doi: 10.1038/s12276-024-01284-1. Epub 2024 Aug 1. Exp Mol Med. 2024. PMID: 39085355 Free PMC article.

The genomic and evolutionary landscapes of anaplastic thyroid carcinoma.

Zeng PYF, Prokopec SD, Lai SY, Pinto N, Chan-Seng-Yue MA, Clifton-Bligh R, Williams MD, Howlett CJ, Plantinga P, Cecchini MJ, Lam AK, Siddiqui I, Wang J, Sun RX, Watson JD, Korah R, Carling T, Agrawal N, Cipriani N, Ball D, Nelkin B, Rooper LM, Bishop JA, Garnis C, Berean K, Nicolson NG, Weinberger P, Henderson YC, Lalansingh CM, Tian M, Yamaguchi TN, Livingstone J, Salcedo A, Patel K, Vizeacoumar F, Datti A, Xi L, Nikiforov YE, Smallridge R, Copland JA, Marlow LA, Hyrcza MD, Delbridge L, Sidhu S, Sywak M, Robinson B, Fung K, Ghasemi F, Kwan K, MacNeil SD, Mendez A, Palma DA, Khan MI, Shaikh M, Ruicci KM, Wehrli B, Winquist E, Yoo J, Mymryk JS, Rocco JW, Wheeler D, Scherer S, Giordano TJ, Barrett JW, Faquin WC, Gill AJ, Clayman G, Boutros PC, Nichols AC. Zeng PYF, et al. Cell Rep. 2024 Mar 26;43(3):113826. doi: 10.1016/j.celrep.2024.113826. Epub 2024 Feb 26. Cell Rep. 2024. PMID: 38412093 Free PMC article.

CHARR efficiently estimates contamination from DNA sequencing data.

Lu W, Gauthier LD, Poterba T, Giacopuzzi E, Goodrich JK, Stevens CR, King D, Daly MJ, Neale BM, Karczewski KJ. Lu W, et al. Am J Hum Genet. 2023 Dec 7;110(12):2068-2076. doi: 10.1016/j.ajhg.2023.10.011. Epub 2023 Nov 23. Am J Hum Genet. 2023. PMID: 38000370 Free PMC article.