Analysis of BRCA2 loss of heterozygosity in tumor tissue using droplet digital polymerase chain reaction

被引：12

作者：

Cochran, Rory L. ^{[1
]}

Cravero, Karen ^{[1
]}

Chu, David ^{[1
]}

Erlanger, Bracha ^{[1
]}

Toro, Patricia Valda ^{[1
]}

Beaver, Julia A. ^{[1
]}

Zabransky, Daniel J. ^{[1
]}

Wong, Hong Yuen ^{[1
]}

Cidado, Justin ^{[1
]}

Croessmann, Sarah ^{[1
]}

Parsons, Heather A. ^{[1
]}

Kim, Minsoo ^{[1
]}

Wheelan, Sarah J. ^{[1
]}

Argani, Pedram ^{[1
]}

Park, Ben Ho ^{[1
]}

机构：

[1] Johns Hopkins Univ, Sch Med, Sidney Kimmel Comprehens Canc Ctr, Baltimore, MD 21287 USA

来源：

HUMAN PATHOLOGY | 2014年 / 45卷 / 07期

基金：

美国国家卫生研究院;

关键词：

Droplet digital PCR; LOH; Familial breast cancer; BRCA2; VUS; UNKNOWN CLINICAL-SIGNIFICANCE; BREAST-CANCER; SEQUENCE VARIANTS; QUANTITATION; CARRIERS; SAMPLES;

D O I：

10.1016/j.humpath.2014.03.013

中图分类号：

R36 [病理学];

学科分类号：

100104 ;

摘要：

Loss-of-heterozygosity (LOH) analysis of archival tumor tissue can aid in determining the clinical significance of BRCA variants. Here we describe an approach for assessing LOH in formalin-fixed, paraffin-embedded (FFPE) tissues using variant-specific probes and droplet digital polymerase chain reaction (ddPCR). We evaluated LOH in 2 related breast cancer patients harboring a rare missense BRCA2 variant of unknown clinical significance (c.6966G>T; M2322I). Conventional PCR followed by Sanger sequencing suggested a change in allelic abundance in the FFPE specimens. However, we found no evidence of LOH as determined by the allelic ratio (wild type variant) for BRCA2 in both patients' archival tumor specimens and adjacent normal control tissues using ddPCR. In summary, these experiments demonstrate the utility of ddPCR to quickly and accurately assess LOH in archival FFPE tumor tissue. (C) 2014 Elsevier Inc. All rights reserved.

引用

页码：1546 / 1550

页数：5

共 15 条

[1] The PIK3CA gene is mutated with high frequency in human breast cancers [J].

Bachman, KE ;

Argani, P ;

Samuels, Y ;

Silliman, N ;

Ptak, J ;

Szabo, S ;

Konishi, H ;

Karakas, B ;

Blair, BG ;

Lin, C ;

Peters, BA ;

Velculescu, VE ;

Park, BH .

CANCER BIOLOGY & THERAPY, 2004, 3 (08) :772-775

[2]

Belgrader P, 2013, CLIN CHEM, V000, P1

[3] Genetic and histopathologic evaluation of BRCA1 and BRCA2 DNA sequence variants of unknown clinical significance [J].

Chenevix-Trench, G ;

Healey, S ;

Lakhani, S ;

Waring, P ;

Cummings, M ;

Brinkworth, R ;

Deffenbaugh, AM ;

Burbidge, LA ;

Pruss, D ;

Judkins, T ;

Scholl, T ;

Bekessy, A ;

Marsh, A ;

Lovelock, P ;

Wong, M ;

Tesoriero, A ;

Renard, H ;

Southey, M ;

Hopper, JL ;

Yannoukakos, K ;

Brown, M ;

Easton, D ;

Tavtigian, SV ;

Goldgars, D ;

Spurdle, AB .

CANCER RESEARCH, 2006, 66 (04) :2019-2027

[4] A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes [J].

Easton, Douglas F. ;

Deffenbaugh, Amie M. ;

Pruss, Dmitry ;

Frye, Cynthia ;

Wenstrup, Richard J. ;

Allen-Brady, Kristina ;

Tavtigian, Sean V. ;

Monteiro, Alvaro N. A. ;

Iversen, Edwin S. ;

Couch, Fergus J. ;

Goldgar, David E. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 81 (05) :873-883

[5] Droplet Digital™ PCR quantitation of HER2 expression in FFPE breast cancer samples [J].

Heredia, Nicholas J. ;

Belgrader, Phillip ;

Wang, Shenglong ;

Koehler, Ryan ;

Regan, Jack ;

Cosman, Angela M. ;

Saxonov, Serge ;

Hindson, Benjamin ;

Tanner, Stephanie C. ;

Brown, Alexandra S. ;

Karlin-Neumann, George .

METHODS, 2013, 59 (01) :S20-S23

[6] High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number [J].

Hindson, Benjamin J. ;

Ness, Kevin D. ;

Masquelier, Donald A. ;

Belgrader, Phillip ;

Heredia, Nicholas J. ;

Makarewicz, Anthony J. ;

Bright, Isaac J. ;

Lucero, Michael Y. ;

Hiddessen, Amy L. ;

Legler, Tina C. ;

Kitano, Tyler K. ;

Hodel, Michael R. ;

Petersen, Jonathan F. ;

Wyatt, Paul W. ;

Steenblock, Erin R. ;

Shah, Pallavi H. ;

Bousse, Luc J. ;

Troup, Camille B. ;

Mellen, Jeffrey C. ;

Wittmann, Dean K. ;

Erndt, Nicholas G. ;

Cauley, Thomas H. ;

Koehler, Ryan T. ;

So, Austin P. ;

Dube, Simant ;

Rose, Klint A. ;

Montesclaros, Luz ;

Wang, Shenglong ;

Stumbo, David P. ;

Hodges, Shawn P. ;

Romine, Steven ;

Milanovich, Fred P. ;

White, Helen E. ;

Regan, John F. ;

Karlin-Neumann, George A. ;

Hindson, Christopher M. ;

Saxonov, Serge ;

Colston, Bill W. .

ANALYTICAL CHEMISTRY, 2011, 83 (22) :8604-8610

[7]

Kaman S, 2010, BREAST CANC RES TREA, V119, P249

[8] Fast and accurate short read alignment with Burrows-Wheeler transform [J].

Li, Heng ;

Durbin, Richard .

BIOINFORMATICS, 2009, 25 (14) :1754-1760

[9] The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data [J].

McKenna, Aaron ;

Hanna, Matthew ;

Banks, Eric ;

Sivachenko, Andrey ;

Cibulskis, Kristian ;

Kernytsky, Andrew ;

Garimella, Kiran ;

Altshuler, David ;

Gabriel, Stacey ;

Daly, Mark ;

DePristo, Mark A. .

GENOME RESEARCH, 2010, 20 (09) :1297-1303

[10] BRCA1 and BRCA2:: 1994 and beyond [J].

Narod, SA ;

Foulkes, WD .

NATURE REVIEWS CANCER, 2004, 4 (09) :665-676

← 1 2 →