Category: 2024

Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations A
By November 1, 2024

Stenton SL, Pejaver V, Bergquist T, Biesecker LG, Byrne AB, Nadeau EAW, Greenblatt MS, Harrison SM, Tavtigian SV, Radivojac P, Brenner SE, O’Donnell-Luria A; ClinGen Sequence Variant Interpretation Working Group. Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations. Genet Med. 2024 Jul 25;26(11):101213. doi: 10.1016/j.gim.2024.101213. Epub ahead of print. PMID: 39030733.

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Poly (ADP-ribose) Polymerase Inhibitor Resistance Driven by Emergence of Polyclonal Mutations With Convergent Evolution: A Molecular Tumor Board Discussion P
By November 1, 2024

Fatteh M, Wehr J, Karaindrou K, Xian RR, Gocke C, Lin MT, Petry D, Visvanathan K, Couzi R, Santa Maria C, Stearns V, Tao JJ, Anagnostou V, Canzoniero JV; and the Johns Hopkins Molecular Tumor Board; Johns Hopkins Molecular Tumor Board. Poly (ADP-ribose) Polymerase Inhibitor Resistance Driven by Emergence of Polyclonal Mutations With Convergent Evolution: …

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SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors S
By November 1, 2024

Palmer T, Kessler MD, Shao XM, Balan A, Yarchoan M, Zaidi N, Lopez-Vidal TY, Saeed AM, Gore J, Azad NS, Jaffee EM, Favorov AV, Anagnostou V, Karchin R, Gaykalova DA, Fertig EJ, Danilova L. SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors. Cancer Res Commun. 2024 Oct 29. doi: 10.1158/2767-9764.CRC-23-0309. Epub ahead of …

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Improving transparency of computational tools for variant effect prediction I
By July 8, 2024

Karchin R, Radivojac P, O’Donnell-Luria A, Greenblatt MS, Tolstorukov MY, Sonkin D. Improving transparency of computational tools for variant effect prediction. Nat Genet. 2024 Jul 2. doi: 10.1038/s41588-024-01821-8. Epub ahead of print. PMID: 38956207.

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Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction A
By June 27, 2024

Lai J, Yang Y, Liu Y, Scharpf RB, Karchin R. Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction. Bioinformatics Advances, 2024 June. doi: 10.1093/bioadv/vbae094. PMID: 38948008; PMCID: PMC11213631.

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3D genomic mapping reveals multifocality of human pancreatic precancers 3
By May 3, 2024

Braxton AM, Kiemen AL, Grahn MP, Forjaz A, Parksong J, Mahesh Babu J, Lai J, Zheng L, Niknafs N, Jiang L, Cheng H, Song Q, Reichel R, Graham S, Damanakis AI, Fischer CG, Mou S, Metz C, Granger J, Liu XD, Bachmann N, Zhu Y, Liu Y, Almagro-Pérez C, Jiang AC, Yoo J, Kim B, …

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CAGI, the critical assessment of genome interpretation, establishes progress and prospects for computational genetic variant interpretation methods. C
By March 28, 2024

The Critical Assessment of Genome Interpretation Consortium. CAGI, the critical assessment of genome interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology 2024 25(1):53. PMID: 38389099 PMCID: PMC10882881

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