Publications:

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Luminal-Type Invasive Carcinoma in Association With Microglandular Adenosis/Atypical Microglandular Adenosis: A Case Report and Molecular Comparison.

Cureus

Jaramillo, Couger C; Nazario-Toole, Ashley A; Xia, Hui H; Adams, Thomas T; Josey, Michelle M

Publication Date: 2023-04

Variant appearance in text: BRCA1: 4636G>A; Asp1546Asn

PubMed Link: 37159793

Variant Present in the following documents:

• Main text

View BVdb publication page

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Evaluation of AlphaFold structure-based protein stability prediction on missense variations in cancer.

Frontiers In Genetics

Keskin Karakoyun, Hilal H; Yüksel, Şirin K ŞK; Amanoglu, Ilayda I; Naserikhojasteh, Lara L; Yeşilyurt, Ahmet A; Yakıcıer, Cengiz C; Timuçin, Emel E; Akyerli, Cemaliye B CB

Publication Date: 2023

Variant appearance in text: BRCA1: D1546N

PubMed Link: 36896237

Variant Present in the following documents:

• Table1.xlsx, sheet 1

View BVdb publication page

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APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP.

Medrxiv : The Preprint Server For Health Sciences

Walker, Logan C LC; de la Hoya, Miguel M; Wiggins, George Ar GA; Lindy, Amanda A; Vincent, Lisa M LM; Parsons, Michael M; Canson, Daffodil M DM; Bis-Brewer, Dana D; Cass, Ashley A; Tchourbanov, Alexander A; Zimmermann, Heather H; Byrne, Alicia B AB; Pesaran, Tina T; Karam, Rachid R; Harrison, Steven M SM; , ; Spurdle, Amanda B AB

Publication Date: 2023-02-26

Variant appearance in text: BRCA1: 4636G>A

PubMed Link: 36865205

Variant Present in the following documents:

• media-10.xlsx, sheet 1

View BVdb publication page

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Analysis of single-nucleotide polymorphisms in genes associated with triple-negative breast cancer.

Frontiers In Genetics

G, Vigneshwaran V; Hasan, Qurratulain Annie QA; Kumar, Rahul R; Eranki, Avinash A

Publication Date: 2022

Variant appearance in text: rs28897691

PubMed Link: 36561320

Variant Present in the following documents:

• Table2.xlsx, sheet 2

View BVdb publication page

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Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria.

American Journal Of Human Genetics

Pejaver, Vikas V; Byrne, Alicia B AB; Feng, Bing-Jian BJ; Pagel, Kymberleigh A KA; Mooney, Sean D SD; Karchin, Rachel R; O'Donnell-Luria, Anne A; Harrison, Steven M SM; Tavtigian, Sean V SV; Greenblatt, Marc S MS; Biesecker, Leslie G LG; Radivojac, Predrag P; Brenner, Steven E SE; ,

Publication Date: 2022-12-01

Variant appearance in text: rs28897691

PubMed Link: 36413997

Variant Present in the following documents:

• mmc2.xlsx, sheet 1

View BVdb publication page

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Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population.

International Journal Of Cancer

Qin, Zixin Z; Li, Jiaheng J; Tam, Benjamin B; Sinha, Siddharth S; Zhao, Bojin B; Bhaskaran, Shanmuga Priya SP; Huang, Teng T; Wu, Xiaobing X; Chian, Jia Sheng JS; Guo, Maoni M; Kou, Si Hoi SH; Lei, Huijun H; Zhang, Li L; Wang, Xiaoyu X; Lagniton, Philip Naderev P PNP; Xiao, Fengxia F; Jiang, Xinyang X; Wang, San Ming SM

Publication Date: 2022-11-17

Variant appearance in text: BRCA1: 4636G>A; Asp1546Asn

PubMed Link: 36385461

Variant Present in the following documents:

• IJC-152-1159-s009.xlsx, sheet 2
• IJC-152-1159-s002.xlsx, sheet 1
• IJC-152-1159-s006.xlsx, sheet 2

View BVdb publication page

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Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2.

Scientific Reports

Aljarf, Raghad R; Shen, Mengyuan M; Pires, Douglas E V DEV; Ascher, David B DB

Publication Date: 2022-06-21

Variant appearance in text: BRCA1: D1546N

PubMed Link: 35729312

Variant Present in the following documents:

• 41598_2022_13508_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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An integrative model for the comprehensive classification of BRCA1 and BRCA2 variants of uncertain clinical significance.

Npj Genomic Medicine

Iversen, Edwin S ES; Lipton, Gary G; Hart, Steven N SN; Lee, Kun Y KY; Hu, Chunling C; Polley, Eric C EC; Pesaran, Tina T; Yussuf, Amal A; LaDuca, Holly H; Chao, Elizabeth E; Karam, Rachid R; Goldgar, David E DE; Couch, Fergus J FJ; Monteiro, Alvaro N A ANA

Publication Date: 2022-06-03

Variant appearance in text: BRCA1: D1546N

PubMed Link: 35665744

Variant Present in the following documents:

• 41525_2022_302_MOESM3_ESM.xlsx, sheet 5
• 41525_2022_Article_302.pdf
• 41525_2022_302_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms.

Nature Cancer

Lehtiö, Janne J; Arslan, Taner T; Siavelis, Ioannis I; Pan, Yanbo Y; Socciarelli, Fabio F; Berkovska, Olena O; Umer, Husen M HM; Mermelekas, Georgios G; Pirmoradian, Mohammad M; Jönsson, Mats M; Brunnström, Hans H; Brustugun, Odd Terje OT; Purohit, Krishna Pinganksha KP; Cunningham, Richard R; Foroughi Asl, Hassan H; Isaksson, Sofi S; Arbajian, Elsa E; Aine, Mattias M; Karlsson, Anna A; Kotevska, Marija M; Gram Hansen, Carsten C; Drageset Haakensen, Vilde V; Helland, Åslaug Å; Tamborero, David D; Johansson, Henrik J HJ; Branca, Rui M RM; Planck, Maria M; Staaf, Johan J; Orre, Lukas M LM

Publication Date: 2021-11

Variant appearance in text: BRCA1: 4636G>A; Asp1546Asn

PubMed Link: 34870237

Variant Present in the following documents:

• EMS133264-supplement-Supplementary_Tables.xlsx, sheet 9

View BVdb publication page

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Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays.

Scientific Reports

Khoruddin, Nurul Ain NA; Noorizhab, Mohd NurFakhruzzaman MN; Teh, Lay Kek LK; Mohd Yusof, Farida Zuraina FZ; Salleh, Mohd Zaki MZ

Publication Date: 2021-08-09

Variant appearance in text: rs28897691

PubMed Link: 34373545

Variant Present in the following documents:

• 41598_2021_95618_MOESM1_ESM.xlsx, sheet 1

View BVdb publication page

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A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases.

Scientific Reports

Magraner-Pardo, Lorena L; Laskowski, Roman A RA; Pons, Tirso T; Thornton, Janet M JM

Publication Date: 2021-07-12

Variant appearance in text: N/A

PubMed Link: 34253785

Variant Present in the following documents:

View BVdb publication page

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Prediction of the functional impact of missense variants in BRCA1 and BRCA2 with BRCA-ML.

Npj Breast Cancer

Hart, Steven N SN; Polley, Eric C EC; Shimelis, Hermella H; Yadav, Siddhartha S; Couch, Fergus J FJ

Publication Date: 2020

Variant appearance in text: BRCA1: 4636G>A; Asp1546Asn

PubMed Link: 32377563

Variant Present in the following documents:

• 41523_2020_159_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".

Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Dines, Jennifer N JN; Shirts, Brian H BH; Slavin, Thomas P TP; Walsh, Tom T; King, Mary-Claire MC; Fowler, Douglas M DM; Pritchard, Colin C CC

Publication Date: 2020-05

Variant appearance in text: BRCA1: D1546N; rs28897691

PubMed Link: 31911673

Variant Present in the following documents:

• 41436_2019_740_MOESM2_ESM.xlsx, sheet 2
• 41436_2019_740_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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TAPES: A tool for assessment and prioritisation in exome studies.

Plos Computational Biology

Xavier, Alexandre A; Scott, Rodney J RJ; Talseth-Palmer, Bente A BA

Publication Date: 2019-10

Variant appearance in text: BRCA1: D1546N; rs28897691

PubMed Link: 31613886

Variant Present in the following documents:

• pcbi.1007453.s002.xlsx, sheet 1
• pcbi.1007453.s004.xlsx, sheet 2

View BVdb publication page

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REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification.

Scientific Reports

Tian, Yuan Y; Pesaran, Tina T; Chamberlin, Adam A; Fenwick, R Bryn RB; Li, Shuwei S; Gau, Chia-Ling CL; Chao, Elizabeth C EC; Lu, Hsiao-Mei HM; Black, Mary Helen MH; Qian, Dajun D

Publication Date: 2019-09-04

Variant appearance in text: BRCA1: 4636G>A; D1546N

PubMed Link: 31484976

Variant Present in the following documents:

• 41598_2019_49224_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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Finding driver mutations in cancer: Elucidating the role of background mutational processes.

Plos Computational Biology

Brown, Anna-Leigh AL; Li, Minghui M; Goncearenco, Alexander A; Panchenko, Anna R AR

Publication Date: 2019-04

Variant appearance in text: BRCA1: D1546N

PubMed Link: 31034466

Variant Present in the following documents:

• pcbi.1006981.s010.xlsx, sheet 1

View BVdb publication page

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Functional Interaction Between BRCA1 and DNA Repair in Yeast May Uncover a Role of RAD50, RAD51, MRE11A, and MSH6 Somatic Variants in Cancer Development.

Frontiers In Genetics

Maresca, Luisa L; Lodovichi, Samuele S; Lorenzoni, Alessandra A; Cervelli, Tiziana T; Monaco, Rossella R; Spugnesi, Laura L; Tancredi, Mariella M; Falaschi, Elisabetta E; Zavaglia, Katia K; Landucci, Elisabetta E; Roncella, Manuela M; Congregati, Caterina C; Gadducci, Angiolo A; Naccarato, Antonio Giuseppe AG; Caligo, Maria Adelaide MA; Galli, Alvaro A

Publication Date: 2018

Variant appearance in text: BRCA1: D1546N

PubMed Link: 30283497

Variant Present in the following documents:

• Main text

View BVdb publication page

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A Bayesian framework for efficient and accurate variant prediction.

Plos One

Qian, Dajun D; Li, Shuwei S; Tian, Yuan Y; Clifford, Jacob W JW; Sarver, Brice A J BAJ; Pesaran, Tina T; Gau, Chia-Ling CL; Elliott, Aaron M AM; Lu, Hsiao-Mei HM; Black, Mary Helen MH

Publication Date: 2018

Variant appearance in text: BRCA1: 4636G>A; D1546N

PubMed Link: 30212499

Variant Present in the following documents:

• pone.0203553.s008.xlsx, sheet 2

View BVdb publication page

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Comprehensive annotation of BRCA1 and BRCA2 missense variants by functionally validated sequence-based computational prediction models.

Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Hart, Steven N SN; Hoskin, Tanya T; Shimelis, Hermela H; Moore, Raymond M RM; Feng, Bingjian B; Thomas, Abigail A; Lindor, Noralane M NM; Polley, Eric C EC; Goldgar, David E DE; Iversen, Edwin E; Monteiro, Alvaro N A ANA; Suman, Vera J VJ; Couch, Fergus J FJ

Publication Date: 2019-01

Variant appearance in text: BRCA1: D1546N

PubMed Link: 29884841

Variant Present in the following documents:

• NIHMS953431-supplement-Table_S2.xls, sheet 1

View BVdb publication page

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Performance of in silico prediction tools for the classification of rare BRCA1/2 missense variants in clinical diagnostics.

Bmc Medical Genomics

Ernst, Corinna C; Hahnen, Eric E; Engel, Christoph C; Nothnagel, Michael M; Weber, Jonas J; Schmutzler, Rita K RK; Hauke, Jan J

Publication Date: 2018-03-27

Variant appearance in text: BRCA1: D1546N

PubMed Link: 29580235

Variant Present in the following documents:

• 12920_2018_353_MOESM1_ESM.xlsx, sheet 1

View BVdb publication page

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Sources of discordance among germ-line variant classifications in ClinVar.

Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Yang, Shan S; Lincoln, Stephen E SE; Kobayashi, Yuya Y; Nykamp, Keith K; Nussbaum, Robert L RL; Topper, Scott S

Publication Date: 2017-10

Variant appearance in text: BRCA1: 4636G>A; Asp1546Asn

PubMed Link: 28569743

Variant Present in the following documents:

• gim201760x7.xlsx, sheet 2

View BVdb publication page

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The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine.

Genome Medicine

Garofalo, Andrea A; Sholl, Lynette L; Reardon, Brendan B; Taylor-Weiner, Amaro A; Amin-Mansour, Ali A; Miao, Diana D; Liu, David D; Oliver, Nelly N; MacConaill, Laura L; Ducar, Matthew M; Rojas-Rudilla, Vanesa V; Giannakis, Marios M; Ghazani, Arezou A; Gray, Stacy S; Janne, Pasi P; Garber, Judy J; Joffe, Steve S; Lindeman, Neal N; Wagle, Nikhil N; Garraway, Levi A LA; Van Allen, Eliezer M EM

Publication Date: 2016-07-26

Variant appearance in text: rs28897691

PubMed Link: 27460824

Variant Present in the following documents:

• 13073_2016_333_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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A Landscape of Pharmacogenomic Interactions in Cancer.

Cell

Iorio, Francesco F; Knijnenburg, Theo A TA; Vis, Daniel J DJ; Bignell, Graham R GR; Menden, Michael P MP; Schubert, Michael M; Aben, Nanne N; Gonçalves, Emanuel E; Barthorpe, Syd S; Lightfoot, Howard H; Cokelaer, Thomas T; Greninger, Patricia P; van Dyk, Ewald E; Chang, Han H; de Silva, Heshani H; Heyn, Holger H; Deng, Xianming X; Egan, Regina K RK; Liu, Qingsong Q; Mironenko, Tatiana T; Mitropoulos, Xeni X; Richardson, Laura L; Wang, Jinhua J; Zhang, Tinghu T; Moran, Sebastian S; Sayols, Sergi S; Soleimani, Maryam M; Tamborero, David D; Lopez-Bigas, Nuria N; Ross-Macdonald, Petra P; Esteller, Manel M; Gray, Nathanael S NS; Haber, Daniel A DA; Stratton, Michael R MR; Benes, Cyril H CH; Wessels, Lodewyk F A LFA; Saez-Rodriguez, Julio J; McDermott, Ultan U; Garnett, Mathew J MJ

Publication Date: 2016-07-28

Variant appearance in text: BRCA1: 4636G>A; D1546N

PubMed Link: 27397505

Variant Present in the following documents:

• mmc3.xlsx, sheet 3

View BVdb publication page

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Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.

Genome Biology

Martelotto, Luciano G LG; Ng, Charlotte Ky CK; De Filippo, Maria R MR; Zhang, Yan Y; Piscuoglio, Salvatore S; Lim, Raymond S RS; Shen, Ronglai R; Norton, Larry L; Reis-Filho, Jorge S JS; Weigelt, Britta B

Publication Date: 2014-10-28

Variant appearance in text: BRCA1: D1546N

PubMed Link: 25348012

Variant Present in the following documents:

• 13059_2014_484_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing.

Nucleic Acids Research

Tessereau, Chloé C; Lesecque, Yann Y; Monnet, Nastasia N; Buisson, Monique M; Barjhoux, Laure L; Léoné, Mélanie M; Feng, Bingjian B; Goldgar, David E DE; Sinilnikova, Olga M OM; Mousset, Sylvain S; Duret, Laurent L; Mazoyer, Sylvie S

Publication Date: 2014-08

Variant appearance in text: rs28897691

PubMed Link: 25034697

Variant Present in the following documents:

• supp_gku639_nar-00908-d-2014-File008.xlsx, sheet 1

View BVdb publication page

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Prevalance of BRCA1 and BRCA2 mutations in familial breast cancer patients in Lebanon.

Hereditary Cancer In Clinical Practice

Jalkh, Nadine N; Nassar-Slaba, Jinane J; Chouery, Eliane E; Salem, Nabiha N; Uhrchammer, Nancy N; Golmard, Lisa L; Stoppa-Lyonnet, Domique D; Bignon, Yves-Jean YJ; Mégarbané, André A

Publication Date: 2012-06-19

Variant appearance in text: BRCA1: D1546N

PubMed Link: 22713736

Variant Present in the following documents:

• Main text
• 1897-4287-10-7.pdf

View BVdb publication page

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A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS).

Human Mutation

Lindor, Noralane M NM; Guidugli, Lucia L; Wang, Xianshu X; Vallée, Maxime P MP; Monteiro, Alvaro N A AN; Tavtigian, Sean S; Goldgar, David E DE; Couch, Fergus J FJ

Publication Date: 2012-01

Variant appearance in text: BRCA1: 4636G>A; Asp1546Asn

PubMed Link: 21990134

Variant Present in the following documents:

• Main text

View BVdb publication page

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A computational method to classify variants of uncertain significance using functional assay data with application to BRCA1.

Cancer Epidemiology, Biomarkers & Prevention : A Publication Of The American Association For Cancer Research, Cosponsored By The American Society Of Preventive Oncology

Iversen, Edwin S ES; Couch, Fergus J FJ; Goldgar, David E DE; Tavtigian, Sean V SV; Monteiro, Alvaro N A AN

Publication Date: 2011-06

Variant appearance in text: BRCA1: D1546N

PubMed Link: 21447777

Variant Present in the following documents:

• Main text

View BVdb publication page

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Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

Mutation Research

Carvalho, Marcelo M; Pino, Maria A MA; Karchin, Rachel R; Beddor, Jennifer J; Godinho-Netto, Martha M; Mesquita, Rafael D RD; Rodarte, Renato S RS; Vaz, Danielle C DC; Monteiro, Viviane A VA; Manoukian, Siranoush S; Colombo, Mara M; Ripamonti, Carla B CB; Rosenquist, Richard R; Suthers, Graeme G; Borg, Ake A; Radice, Paolo P; Grist, Scott A SA; Monteiro, Alvaro N A AN; Billack, Blase B

Publication Date: 2009-01-15

Variant appearance in text: BRCA1: D1546N

PubMed Link: 18992264

Variant Present in the following documents:

• Main text

View BVdb publication page

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Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis.

Cancer Research

Carvalho, Marcelo A MA; Marsillac, Sylvia M SM; Karchin, Rachel R; Manoukian, Siranoush S; Grist, Scott S; Swaby, Ramona F RF; Urmenyi, Turan P TP; Rondinelli, Edson E; Silva, Rosane R; Gayol, Luis L; Baumbach, Lisa L; Sutphen, Rebecca R; Pickard-Brzosowicz, Jennifer L JL; Nathanson, Katherine L KL; Sali, Andrej A; Goldgar, David D; Couch, Fergus J FJ; Radice, Paolo P; Monteiro, Alvaro N A AN

Publication Date: 2007-02-15

Variant appearance in text: BRCA1: D1546N

PubMed Link: 17308087

Variant Present in the following documents:

• Main text

View BVdb publication page

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Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral.

Journal Of Medical Genetics

Tavtigian, S V SV; Deffenbaugh, A M AM; Yin, L L; Judkins, T T; Scholl, T T; Samollow, P B PB; de Silva, D D; Zharkikh, A A; Thomas, A A

Publication Date: 2006-04

Variant appearance in text: BRCA1: D1546N

PubMed Link: 16014699

Variant Present in the following documents:

• Main text

View BVdb publication page

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