The Jorge Reis-Filho Lab

Cancer-Causative Mutations Occurring in Early Embryogenesis. Pareja F, Ptashkin RN, Brown DN, Derakhshan F, Selenica P, da Silva EM, Gazzo AM, Da Cruz Paula A, Breen K, Shen R, Marra A, Zehir A, Benayed R, Berger MF, Ceyhan-Birsoy O, Jairam S, Sheehan M, Patel U, Kemel Y, Casanova-Murphy J, Schwartz CJ, Vahdatinia M, Comen E, Borsu L, Pei X, Riaz N, Abramson DH, Weigelt B, Walsh MF, Hadjantonakis AK, Ladanyi M, Offit K, Stadler ZK, Robson ME, Reis-Filho JS*, Mandelker D*. Cancer Discov 2022;12:949-957. PMCID: PMC8983494. *: Corresponding authors.

APOBEC mutagenesis, kataegis, chromothripsis in EGFR-mutant osimertinib-resistant lung adenocarcinomas.  Selenica P, Marra A, Choudhury NJ, Gazzo A, Falcon CJ, Patel J, Pei X, Zhu Y, Ng CKY, Curry M, Heller G, Zhang YK, Berger MF, Ladanyi M, Rudin CM, Chandarlapaty S, Lovly CM, Reis-Filho JS*, Yu HA*.  Ann Oncol 2022;33:1284-1295. PMID: 36089134. *: Corresponding authors.

High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants. Razavi P, Li BT, Brown DN, Jung B, Hubbell E, Shen R, Abida W, Juluru K, De Bruijn I, Hou C, Venn O, Lim R, Anand A, Maddala T, Gnerre S, Vijaya Satya R, Liu Q, Shen L, Eattock N, Yue J, Blocker AW, Lee M, Sehnert A, Xu H, Hall MP, Santiago-Zayas A, Novotny WF, Isbell JM, Rusch VW, Plitas G, Heerdt AS, Ladanyi M, Hyman DM, Jones DR, Morrow M, Riely GJ, Scher HI, Rudin CM, Robson ME, Diaz LA Jr, Solit DB, Aravanis AM, Reis-Filho JS. Nat Med 2019; 25:1928-1937. PMCID: PMC7061455.

Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. Martelotto LG, Baslan T, Kendall J, Geyer FC, Burke KA, Spraggon L, Piscuoglio S, Chadalavada K, Nanjangud G, Ng CK, Moody P, D’Italia S, Rodgers L, Cox H, da Cruz Paula A, Stepansky A, Schizas M, Wen HY, King TA, Norton L, Weigelt B, Hicks JB, Reis-Filho JS. Nat Med 2017; 23:376-385. PMCID: PMC5608257.

Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands. Weinreb I, Piscuoglio S, Martelotto LG, Waggott D, Ng CK, Perez-Ordonez B, Harding NJ, Alfaro J, Chu KC, Viale A, Fusco N, da Cruz Paula A, Marchio C, Sakr RA, Lim R, Thompson LD, Chiosea SI, Seethala RR, Skalova A, Stelow EB, Fonseca I, Assaad A, How C, Wang J, de Borja R, Chan-Seng-Yue M, Howlett CJ, Nichols AC, Wen YH, Katabi N, Buchner N, Mullen L, Kislinger T, Wouters BG, Liu FF, Norton L, McPherson JD, Rubin BP, Clarke BA, Weigelt B, Boutros PC, Reis-Filho JS. Nat Genet 2014; 46:1166-9.