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Items: 26

1.

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

Tian Y, Pesaran T, Chamberlin A, Fenwick RB, Li S, Gau CL, Chao EC, Lu HM, Black MH, Qian D.

Sci Rep. 2019 Sep 4;9(1):12752. doi: 10.1038/s41598-019-49224-8.

2.

A clinical guide to hereditary cancer panel testing: evaluation of gene-specific cancer associations and sensitivity of genetic testing criteria in a cohort of 165,000 high-risk patients.

LaDuca H, Polley EC, Yussuf A, Hoang L, Gutierrez S, Hart SN, Yadav S, Hu C, Na J, Goldgar DE, Fulk K, Smith LP, Horton C, Profato J, Pesaran T, Gau CL, Pronold M, Davis BT, Chao EC, Couch FJ, Dolinsky JS.

Genet Med. 2019 Aug 13. doi: 10.1038/s41436-019-0633-8. [Epub ahead of print]

PMID:
31406321
3.

Tumour characteristics provide evidence for germline mismatch repair missense variant pathogenicity.

Li S, Qian D, Thompson BA, Gutierrez S, Wu S, Pesaran T, LaDuca H, Lu HM, Chao EC, Black MH.

J Med Genet. 2019 Aug 7. pii: jmedgenet-2019-106096. doi: 10.1136/jmedgenet-2019-106096. [Epub ahead of print]

PMID:
31391288
4.

p53 major hotspot variants are associated with poorer prognostic features in hereditary cancer patients.

Fortuno C, Pesaran T, Dolinsky J, Yussuf A, McGoldrick K, Kho PF, James PA, Spurdle AB.

Cancer Genet. 2019 Jun;235-236:21-27. doi: 10.1016/j.cancergen.2019.05.002. Epub 2019 Jun 6.

PMID:
31296311
5.

Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: an ENIGMA report.

Lopez-Perolio I, Leman R, Behar R, Lattimore V, Pearson JF, Castéra L, Martins A, Vaur D, Goardon N, Davy G, Garre P, García-Barberán V, Llovet P, Pérez-Segura P, Díaz-Rubio E, Caldés T, Hruska KS, Hsuan V, Wu S, Pesaran T, Karam R, Vallon-Christersson J, Borg A, Investigators K, Valenzuela-Palomo A, Velasco EA, Southey M, Vreeswijk MPG, Devilee P, Kvist A, Spurdle AB, Walker LC, Krieger S, de la Hoya M.

J Med Genet. 2019 Jul;56(7):453-460. doi: 10.1136/jmedgenet-2018-105834. Epub 2019 Mar 19.

6.

Two Missense Variants Detected in Breast Cancer Probands Preventing BRCA2-PALB2 Protein Interaction.

Caleca L, Catucci I, Figlioli G, De Cecco L, Pesaran T, Ward M, Volorio S, Falanga A, Marchetti M, Iascone M, Tondini C, Zambelli A, Azzollini J, Manoukian S, Radice P, Peterlongo P.

Front Oncol. 2018 Oct 25;8:480. doi: 10.3389/fonc.2018.00480. eCollection 2018.

7.

Gene-specific criteria for PTEN variant curation: Recommendations from the ClinGen PTEN Expert Panel.

Mester JL, Ghosh R, Pesaran T, Huether R, Karam R, Hruska KS, Costa HA, Lachlan K, Ngeow J, Barnholtz-Sloan J, Sesock K, Hernandez F, Zhang L, Milko L, Plon SE, Hegde M, Eng C.

Hum Mutat. 2018 Nov;39(11):1581-1592. doi: 10.1002/humu.23636.

PMID:
30311380
8.

Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline CDH1 sequence variants.

Lee K, Krempely K, Roberts ME, Anderson MJ, Carneiro F, Chao E, Dixon K, Figueiredo J, Ghosh R, Huntsman D, Kaurah P, Kesserwan C, Landrith T, Li S, Mensenkamp AR, Oliveira C, Pardo C, Pesaran T, Richardson M, Slavin TP, Spurdle AB, Trapp M, Witkowski L, Yi CS, Zhang L, Plon SE, Schrader KA, Karam R.

Hum Mutat. 2018 Nov;39(11):1553-1568. doi: 10.1002/humu.23650.

PMID:
30311375
9.

A Bayesian framework for efficient and accurate variant prediction.

Qian D, Li S, Tian Y, Clifford JW, Sarver BAJ, Pesaran T, Gau CL, Elliott AM, Lu HM, Black MH.

PLoS One. 2018 Sep 13;13(9):e0203553. doi: 10.1371/journal.pone.0203553. eCollection 2018.

10.

Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion.

Abou Tayoun AN, Pesaran T, DiStefano MT, Oza A, Rehm HL, Biesecker LG, Harrison SM; ClinGen Sequence Variant Interpretation Working Group (ClinGen SVI).

Hum Mutat. 2018 Nov;39(11):1517-1524. doi: 10.1002/humu.23626. Epub 2018 Sep 7.

PMID:
30192042
11.

Correction: DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes.

Richardson ME, Chong H, Mu W, Conner BR, Hsuan V, Willett S, Lam S, Tsai P, Pesaran T, Chamberlin AC, Park MS, Gray P, Karam R, Elliott A.

Genet Med. 2019 Jul;21(7):1669. doi: 10.1038/s41436-018-0276-1.

PMID:
30127414
12.

Triple-Negative Breast Cancer Risk Genes Identified by Multigene Hereditary Cancer Panel Testing.

Shimelis H, LaDuca H, Hu C, Hart SN, Na J, Thomas A, Akinhanmi M, Moore RM, Brauch H, Cox A, Eccles DM, Ewart-Toland A, Fasching PA, Fostira F, Garber J, Godwin AK, Konstantopoulou I, Nevanlinna H, Sharma P, Yannoukakos D, Yao S, Feng BJ, Tippin Davis B, Lilyquist J, Pesaran T, Goldgar DE, Polley EC, Dolinsky JS, Couch FJ.

J Natl Cancer Inst. 2018 Aug 1;110(8):855-862. doi: 10.1093/jnci/djy106.

13.

DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes.

Richardson ME, Chong H, Mu W, Conner BR, Hsuan V, Willett S, Lam S, Tsai P, Pesaran T, Chamberlin AC, Park MS, Gray P, Karam R, Elliott A.

Genet Med. 2019 Mar;21(3):683-693. doi: 10.1038/s41436-018-0092-7. Epub 2018 Jul 28. Erratum in: Genet Med. 2018 Aug 20;:.

14.

Advocating for the consumer: clinical confirmation of all direct-to-consumer raw data alterations remains critical.

Tandy-Connor S, Krempely K, Pesaran T, LaDuca H, Guiltinan J, Davis BT.

Genet Med. 2019 Mar;21(3):760-761. doi: 10.1038/s41436-018-0095-4. Epub 2018 Jun 27. No abstract available.

PMID:
29950595
15.

Improved, ACMG-compliant, in silico prediction of pathogenicity for missense substitutions encoded by TP53 variants.

Fortuno C, James PA, Young EL, Feng B, Olivier M, Pesaran T, Tavtigian SV, Spurdle AB.

Hum Mutat. 2018 Aug;39(8):1061-1069. doi: 10.1002/humu.23553. Epub 2018 Jun 5.

16.

Multigene Hereditary Cancer Panels Reveal High-Risk Pancreatic Cancer Susceptibility Genes.

Hu C, LaDuca H, Shimelis H, Polley EC, Lilyquist J, Hart SN, Na J, Thomas A, Lee KY, Davis BT, Black MH, Pesaran T, Goldgar DE, Dolinsky JS, Couch FJ.

JCO Precis Oncol. 2018;2. doi: 10.1200/PO.17.00291. Epub 2018 Jul 25.

17.

Somatic TP53 variants frequently confound germ-line testing results.

Weitzel JN, Chao EC, Nehoray B, Van Tongeren LR, LaDuca H, Blazer KR, Slavin T, Facmg DABMD, Pesaran T, Rybak C, Solomon I, Niell-Swiller M, Dolinsky JS, Castillo D, Elliott A, Gau CL, Speare V, Jasperson K.

Genet Med. 2018 Aug;20(8):809-816. doi: 10.1038/gim.2017.196. Epub 2017 Nov 30.

18.

Associations Between Cancer Predisposition Testing Panel Genes and Breast Cancer.

Couch FJ, Shimelis H, Hu C, Hart SN, Polley EC, Na J, Hallberg E, Moore R, Thomas A, Lilyquist J, Feng B, McFarland R, Pesaran T, Huether R, LaDuca H, Chao EC, Goldgar DE, Dolinsky JS.

JAMA Oncol. 2017 Sep 1;3(9):1190-1196. doi: 10.1001/jamaoncol.2017.0424.

19.

Clinical laboratories collaborate to resolve differences in variant interpretations submitted to ClinVar.

Harrison SM, Dolinsky JS, Knight Johnson AE, Pesaran T, Azzariti DR, Bale S, Chao EC, Das S, Vincent L, Rehm HL.

Genet Med. 2017 Oct;19(10):1096-1104. doi: 10.1038/gim.2017.14. Epub 2017 Mar 16.

20.

Efforts Toward Consensus Variant Interpretation by Commercial Laboratories.

Dolinsky JS, Hruska KS, Pesaran T, Richardson ME, Klein RT, Solomon BD, Gau CL.

J Clin Oncol. 2017 Apr 10;35(11):1261-1262. doi: 10.1200/JCO.2016.71.2505. Epub 2017 Jan 30. No abstract available.

PMID:
28135139
21.

Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes.

Pesaran T, Karam R, Huether R, Li S, Farber-Katz S, Chamberlin A, Chong H, LaDuca H, Elliott A.

Int J Breast Cancer. 2016;2016:2469523. Epub 2016 Oct 16. Review.

22.

Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms.

de la Hoya M, Soukarieh O, López-Perolio I, Vega A, Walker LC, van Ierland Y, Baralle D, Santamariña M, Lattimore V, Wijnen J, Whiley P, Blanco A, Raponi M, Hauke J, Wappenschmidt B, Becker A, Hansen TV, Behar R, Investigators K, Niederacher D, Arnold N, Dworniczak B, Steinemann D, Faust U, Rubinstein W, Hulick PJ, Houdayer C, Caputo SM, Castera L, Pesaran T, Chao E, Brewer C, Southey MC, van Asperen CJ, Singer CF, Sullivan J, Poplawski N, Mai P, Peto J, Johnson N, Burwinkel B, Surowy H, Bojesen SE, Flyger H, Lindblom A, Margolin S, Chang-Claude J, Rudolph A, Radice P, Galastri L, Olson JE, Hallberg E, Giles GG, Milne RL, Andrulis IL, Glendon G, Hall P, Czene K, Blows F, Shah M, Wang Q, Dennis J, Michailidou K, McGuffog L, Bolla MK, Antoniou AC, Easton DF, Couch FJ, Tavtigian S, Vreeswijk MP, Parsons M, Meeks HD, Martins A, Goldgar DE, Spurdle AB.

Hum Mol Genet. 2016 Jun 1;25(11):2256-2268. Epub 2016 Mar 23.

23.

ClinGen and Genetic Testing.

Karam R, Pesaran T, Chao E.

N Engl J Med. 2015 Oct;373(14):1376-7. doi: 10.1056/NEJMc1508700. No abstract available.

PMID:
26422737
24.

Processed Pseudogene Confounding Deletion/Duplication Assays for SMAD4.

Millson A, Lewis T, Pesaran T, Salvador D, Gillespie K, Gau CL, Pont-Kingdon G, Lyon E, Bayrak-Toydemir P.

J Mol Diagn. 2015 Sep;17(5):576-82. doi: 10.1016/j.jmoldx.2015.05.005. Epub 2015 Jul 10.

PMID:
26165824
25.

Utilization of multigene panels in hereditary cancer predisposition testing: analysis of more than 2,000 patients.

LaDuca H, Stuenkel AJ, Dolinsky JS, Keiles S, Tandy S, Pesaran T, Chen E, Gau CL, Palmaer E, Shoaepour K, Shah D, Speare V, Gandomi S, Chao E.

Genet Med. 2014 Nov;16(11):830-7. doi: 10.1038/gim.2014.40. Epub 2014 Apr 24.

26.

The Diet1 locus confers protection against hypercholesterolemia through enhanced bile acid metabolism.

Phan J, Pesaran T, Davis RC, Reue K.

J Biol Chem. 2002 Jan 4;277(1):469-77. Epub 2001 Oct 26.

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