12968-Breman, Amy
Faculty

Amy M. Breman, PhD

Associate Professor of Clinical Medical & Molecular Genetics

Address
IB 354C
MMGE
IN
Indianapolis, IN

Bio

As a co-director of the Indiana University Cytogenetics Laboratories, my responsibilities include the review and sign-out of cytogenetic, FISH and chromosomal microarray (CMA) cases; helping the lab to uphold CLIA and CAP standards, including participation in QA/QC monitoring, laboratory inspections (both internal and external) and proficiency testing. I am also involved in monitoring the work performed by the laboratory staff, including review and revision of protocols when needed, troubleshooting laboratory procedures, monitoring the training progress of new employees and reviewing the quality of test results generated by the laboratory.  From an education standpoint, I regularly participate in training for ABMGG fellows and visiting pathology residents, genetic counseling student course lectures and employee continuing education activities.

Key Publications

Castelluccio VJ, Vetrini1 F, Lynnes T, Holloway L, Wilson T, Graham BH, Sapp K, Belonis A, Breman A, Schwartz C, Pratt VM, Weaver DD. An unusual cause for Coffin-Lowry syndrome – three brothers with a novel microduplication in RPS6KA3. Am J Med Genet A. 2019 Dec;179(12):2357-2364.

 

Vossaert L, Wang Q, Salman R, McCombs AK, Patel V, Qu C, Mancini MA, Edwards DP, Malovannaya A, Liu P, Shaw CA, Levy B, Wapner RJ, Bi W, Breman AM, Van den Veyver IB, Beaudet A. Validation studies for single circulating trophoblast (SCT) genetic testing as a form of noninvasive prenatal diagnosis. Am J Hum Genet. 2019 Nov 26.

 

Arya P, Wilson T, Parent JJ, Ware, SM, Breman A, Helm BM. An Adult Female with 5q34-q35.2 Deletion: A Rare Syndromic Presentation of Left Ventricular Non-Compaction and Congenital Heart Disease. Eur J Med Genet. 2019 Oct 22:103797.

 

A.V. Dharmadhikari, P.Liu, Hongzheng Dai, Sami Al Masri, J. Scull, J.E. Posey, W. He, F. Vetrini, A. Braxton, P.Ward, T. Chiang, Chunjing Qu, C. Shaw, J.L. Smith, S. Lalani, P.Stankiewicz, S.W. Cheung, C. Bacino, A. Patel, A.M. Breman, X.Wang, L. Meng, R.Xiao, F. Xia, D. Muzny, R.A. Gibbs, A.L. Beaudet, C.M. Eng, J.R. Lupski, Y. Yang, W. Bi. Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. Genome Med. 2019 May 17;11(1):30.

 

Lobashevsky A, Krueger M, Britton R, Littrell C, Susmita S, Cui C, Kashi Z, Martin R, Breman A, Farag S. Pre-transplant HLA typing revealed loss of heterozygosity in the major histocompatibility complex (MHC) in a patient with acute myeloid leukemia. Hum Immunol. 2019 Apr;80(4):257-262.

 

Zhang J, Li J, Saucier JB, Feng Y, Jiang Y, Sinson J, McCombs AK, Schmitt ES, Peacock S, Chen S, Dai H, Ge X, Wang G, Shaw CA, Mei H, Breman A, Xia F, Yang Y, Purgason A, Pourpak A, Chen Z, Wang X, Wang Y, Kulkarni S, Choy KW, Wapner RJ, Van den Veyver IB, Beaudet A, Parmar S, Wong LJ, Eng CM. Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA. Nature Medicine. 2019 Mar;25(3):439-447.

 

Yuan B, Neira J, Pehlivan D, Santiago-Sim T, Song X, Rosenfeld J, Posey JE, Patel V, Jin W, Adam MP, Baple EL, Dean J, Fong CT, Hickey SE, Hudgins L, Leon E, Madan-Khetarpal S, Rawlins L, Rustad CF, Stray-Pedersen A, Tveten K, Wenger O, Diaz J, Jenkins L, Martin L, McGuire M, Pietryga M, Ramsdell L, Slattery L; DDD Study, Abid F, Bertuch AA, Grange D, Immken L, Schaaf CP, Van Esch H, Bi W, Cheung SW, Breman AM, Smith JL, Shaw C, Crosby AH, Eng C, Yang Y, Lupski JR, Xiao R, Liu P. Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. Genet Med. 2019 Mar;21(3):663-675.

 

Vossaert L, Wang Q, Salman R, Zhuo X, Qu C, Henke D, Seubert R, Chow J, U'ren L, Enright B, Stilwell J, Kaldjian E, Yang Y, Shaw C, Levy B, Wapner R, Breman A, Van den Veyver I, Beaudet A. Reliable detection of subchromosomal deletions and duplications using cell-based noninvasive prenatal testing. Prenatal Diagnosis. 2018 Dec;38(13):1069-1078.

 

Gu S, Jernegan M, Van den Veyver IB, Peacock S, Smith J, Breman A. Chromosomal microarray analysis on direct CVS can be complicated by confined placental mosaicism for aneuploidy and microdeletions. Prenatal Diagnosis. 2018 Oct;38(11):858-865.

 

Song X, Beck CR, Du R, Campbell IM, Coban-Akdemir Z, Gu S, Breman AM, Stankiewicz P, Ira G, Shaw CA, Lupski JR. Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements. Genome Res. 2018 Aug;28(8):1228-1242.

 

Pillai NR, Marafi D, Monteiro SA, Parnes M, Chandy BM, Patel A, Bacino CA, Breman AM, Burrage LC. Novel deletion of 6p21.31p21.1 associated with laryngeal cleft, developmental delay, dysmorphic features and vascular anomaly. Eur J Med Genet. 2018 Aug 22.

 

Gennarino VA, Palmer EE, McDonell LM, Wang L, Adamski CJ, Koire A, See L, Chen CA, Schaaf CP, Rosenfeld JA, Panzer JA, Moog U, Hao S, Bye A, Kirk EP, Stankiewicz P, Breman AM, McBride A, Kandula T, Dubbs HA, Macintosh R, Cardamone M, Zhu Y, Ying K, Dias KR, Cho MT, Henderson LB, Baskin B, Morris P, Tao J, Cowley MJ, Dinger ME, Roscioli T, Caluseriu O, Suchowersky O, Sachdev RK, Lichtarge O, Tang J, Boycott KM, Holder JL Jr, Zoghbi HY. A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures. Cell. 2018 Feb 22;172(5):924-936.

 

Petersen AK, Cheung SW, Smith JL, Bi W, Ward PA, Peacock S, Braxton A, Van Den Veyver IB, Breman AM. Positive predictive value estimates for cell-free noninvasive prenatal screening from data of a large referral genetic diagnostic laboratory. Am J Obstet Gynecol. 2017 Oct 13.

 

Case Report in Hematology: A new case of adult Acute Myeloid Leukemia with t(3;3)(p24;q26). B. Yuan, J. Smith, A. Ewton, R. Pingali, A. Zieske, A. Breman. Accepted to Atlas of Genetics and Cytogenetics in Oncology and Haematology, Nov 2017.

 

Stankiewicz P, Khan TN, Szafranski P, Slattery L, Streff H, Vetrini F, Bernstein JA, Brown CW, Rosenfeld JA, Rednam S, Scollon S, Bergstrom KL, Parsons DW, Plon SE, Vieira MW, Quaio CRDC, Baratela WAR, Acosta Guio JC, Armstrong R, Mehta SG, Rump P, Pfundt R, Lewandowski R, Fernandes EM, Shinde DN, Tang S, Hoyer J, Zweier C, Reis A, Bacino CA, Xiao R, Breman AM, Smith JL; Deciphering Developmental Disorders Study, Katsanis N, Bostwick B, Popp B, Davis EE, Yang Y. Haploinsufficiency of the Chromatin Remodeler BPTF Causes Syndromic Developmental and Speech Delay, Postnatal Microcephaly, and Dysmorphic Features. Am J Hum Genet. 2017 Oct 5;101(4):503-515.

 

Novel deletion of 6p21.31p21.1 associated with laryngeal cleft, developmental delay, dysmorphic features and vascular anomaly. N. Pillai, C. A. Bacino, A. M. Breman, A. Patel, S. Monteiro, M.Parnes, D.Marafie, L. C. Burrage. Submitted, Am J Med Genet A, Sept 2017.

 

 

Gambin T, Yuan B, Bi W, Liu P, Rosenfeld JA, Coban-Akdemir Z, Pursley AN, Nagamani SCS, Marom R, Golla S, Dengle L, Petrie HG, Matalon R, Emrick L, Proud MB, Treadwell-Deering D, Chao HT, Koillinen H, Brown C, Urraca N, Mostafavi R, Bernes S, Roeder ER, Nugent KM, Bader PI, Bellus G, Cummings M, Northrup H, Ashfaq M, Westman R, Wildin R, Beck AE, Immken L, Elton L, Varghese S, Buchanan E, Faivre L, Lefebvre M, Schaaf CP, Walkiewicz M, Yang Y, Kang SL, Lalani SR, Bacino CA, Beaudet AL, Breman AM, Smith JL, Cheung SW, Lupski JR, Patel A, Shaw CA, Stankiewicz P. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med. 2017 Sep 21;9(1):83.

 

Chen Y, Bartanus J, Liang D, Zhu H, Breman AM, Smith JL, Wang H, Ren Z, Patel A, Stankiewicz P, Cram DS, Cheung SW, Wu L, Yu F. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat. 2017 Jun;38(6):669-677.

 

Liu P, Yuan B, Carvalho CM, Wuster A, Walter K, Zhang L, Gambin T, Chong Z, Campbell IM, Coban Akdemir Z, Gelowani V, Writzl K, Bacino CA, Lindsay SJ, Withers M, Gonzaga-Jauregui C, Wiszniewska J, Scull J, Stankiewicz P, Jhangiani SN, Muzny DM, Zhang F, Chen K, Gibbs RA, Rautenstrauss B, Cheung SW, Smith J, Breman A, Shaw CA, Patel A, Hurles ME, Lupski JR. An Organismal CNV Mutator Phenotype Restricted to Early Human Development. Cell. 2017 Feb 23;168(5):830-842.e7.

 

Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magriñá MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SW, Carvalho CM, Stankiewicz P, Lupski JR. Mechanisms for Complex Chromosomal Insertions. PLoS Genet. 2016 Nov 23;12(11):e1006446.

 

Kølvraa S, Singh R, Normand EA, Qdaisat S, Van denVeyver IB, Jackson L, Hatt L, Schelde P, Uldbjerg N, Vestergaard EM, Zhao L, Chen R, Shaw CA, Breman AM, Beaudet AL. Genome-wide copy number analysis on DNA from fetal cells isolated from the blood of pregnant women. Prenat Diagn. 2016 Dec;36(12):1127-1134.

 

Amy M. Breman, Jennifer C. Chow, Lance U’Ren, Elizabeth A. Normand, Sadeem Qdaisat, Li Zhao, David M. Henke, Rui Chen, Chad A. Shaw, Laird Jackson, Yaping Yang, Liesbeth Vossaert, Rachel H.V. Needham, Daniel Campton, Jeffrey L. Werbin, Ron C. Seubert, Ignatia B. Van den Veyver, Jackie L. Stilwell, Eric P. Kaldjian, Arthur L. Beaudet. Evidence for feasibility of fetal trophoblastic cell-based noninvasive prenatal testing. Prenat Diagn. 2016 Nov;36(11):1009-1019.

 

Bi W, Cheung SW, Breman AM, Bacino CA. 4p16.3 microdeletions and microduplications detected by chromosomal microarray analysis: New insights into mechanisms and critical regions. Am J Med Genet A. 2016 Oct;170(10):2540-50.

 

Scott DA, Hernandez-Garcia A, Azamian MS, Jordan VK, Kim BJ, Starkovich M, Zhang J, Wong LJ, Darilek SA, Breman AM, Yang Y, Lupski JR, Jiwani AK, Das B, Lalani SR, Iglesias AD, Rosenfeld JA, Xia F. Congenital heart defects and left ventricular non-compaction in males with loss-of-function variants in NONO. J Med Genet. 2017 Jan;54(1):47-53.

 

Normand, E., Qdaisat, S., Bi, W., Shaw, C., Van den Veyver, I., Beaudet, A., Breman, A. (2016) Comparison of three whole genome amplification methods for detection of genomic aberrations in single cells. Prenat Diagn. 2016 Sep;36(9):823-30.

 

Posey J, Mohrbacher N,  Smith JL, Patel A, Potocki L, Breman AM. Triploidy mosaicism (45,X/68,XX) in an infant presenting with failure to thrive. Am J Med Genet A. 2016 Mar;170(3):694-8.

 

Daniel E Campton, Arturo B Ramirez, Joshua J Nordberg, Nick Drovetto, Alisa C Clein, Paulina Varshavskaya, Barry H Friemel, Steve Quarre, Amy Breman, Michael Dorschner, Sibel Blau, C. Anthony Blau, Daniel E Sabath, Jackie L Stilwell and Eric P Kaldjian. High-recovery visual identification and single-cell retrieval of circulating tumor cells for genomic analysis using a dual-technology platform integrated with automated immunofluorescence staining. BMC Cancer. 2015 May 6;15:360.

 

Han K, Holder JL Jr, Schaaf CP, Lu H, Chen H, Kang H, Tang J, Wu Z, Hao S, Cheung SW, Yu P, Sun H, Breman AM, Patel A, Lu HC, Zoghbi HY. SHANK3 overexpression causes manic-like behaviour with unique pharmacogenetic properties. Nature. 2013 Nov 7;503(7474):72-7.

 

Campbell IM, Rao M, Arredondo SD, Lalani SR, Xia Z, Kang SH, Bi W, Breman AM, Smith JL, Bacino CA, Beaudet AL, Patel A, Cheung SW, Lupski JR, Stankiewicz P, Ramocki MB, Shaw CA. Fusion of large-scale genomic knowledge and frequency data computationally prioritizes variants in epilepsy. PLoS Genet. 2013;9(9):e1003797.

 

Piotr Dittwald, Tomasz Gambin, Przemyslaw Szafranski, Jian Li, Stephen Amato, Michael Y. Divon, Lisa Ximena Rodríguez Rojas, Lindsay E. Elton, Daryl A. Scott1, Christian P. Schaaf, Wilfredo Torres-Martinez, Abby K. Stevens, Jill A. Rosenfeld, Satish Agadi, David Francis, Sung-Hae L. Kang, Amy Breman, Seema R. Lalani, Carlos A. Bacino, Weimin Bi, Aleksandar Milosavljevic, Arthur L. Beaudet, Ankita Patel, Chad A. Shaw, James R. Lupski, Anna Gambin, Sau Wai Cheung, Pawel Stankiewicz. NAHR-mediated copy-number variants in a clinical population: mechanistic insights into both genomic disorders and Mendelizing traits. Genome Res. 2013 Sep;23(9):1395-409.

 

Kihoon Han, J. Lloyd Holder, Jr., Christian P. Schaaf, Hui Lu, Hongmei Chen, Hyojin Kang, Jianrong Tang, Zhenyu Wu, Sau Wai Cheung, Peng Yu, Hao Sun, Amy M. Breman, Ankita Patel, Hui-Chen Lu & Huda Y. Zoghbi. SHANK3 overexpression causes manic-like behaviour with unique pharmacogenetic properties. Nature. 2013 Nov 7;503(7474):72-7.

 

Amy Breman and Ankita Patel. Preparation of Chorionic Villus Samples for Metaphase Chromosome Analysis and Chromosomal Microarray Analysis. Current Protocols in Human Genetics 8.3.1-8.3.9, October 2012. (Invited article)

 

Breman A, Pursley AN, Hixson P, Bi W, Ward P, Bacino CA, Shaw C, Lupski JR, Beaudet A, Patel A, Cheung SW, Van den Veyver I. Prenatal chromosomal microarray analysis in a diagnostic laboratory; experience with >1000 cases and review of the literature. Prenat Diagn. 2012 Apr;32(4):351-61. doi: 10.1002/pd.3861.

 

W Bi, A Breman, C Shaw, P Stankiewicz, T Gambin, G Fruhman, X Lu, Z Ou, M Wither, J Sederstrom, J Wiszniewska, C Eng, A Patel, SW Cheung, L Jackson, J Lupski, I Van den Veyver, A Beaudet. Detection of ≥ 1 Mb microdeletions and microduplications in a single cell using custom oligonucleotide arrays: Relevance to noninvasive prenatal testing. Prenat Diagn. 2012 Jan;32(1):10-20.

 

Breman AM, Ramocki MB, Kang SH, Williams M, Freedenberg D, Patel A, Bader PI, Cheung SW. MECP2 duplications in six patients with complex sex chromosome rearrangements. Eur J Hum Genet 2011 Oct;19(10):1110.

 

Oshima J, Lee JA, Breman AM, Fernandes PH, Babovic-Vuksanovic D, Ward PA, Wolfe LA, Eng CM, Del Gaudio D. LCR-initiated rearrangements at the IDS locus, completed with Alu-mediated recombination or non-homologous end joining. J Hum Genet. 2011 Jul;56(7):516-23.

 

Breman AM, Probst FJ, Blazo MA, Schaaf CP, Roney EK, Craigen WJ, Bacino CA, Cheung SW. Identification of complex inv 18 rearrangements by FISH and array CGH in two cases with apparent isochromosome 18q: Case reports. Am J Med Genet A.  2011 Jun;155A(6):1465-8.

 

Ou Z, Stankiewicz P, Xia Z, Breman AM, Dawson B, Wiszniewska J, Szafranski P, Cooper ML, Rao M, Shao L, South ST, Coleman K, Fernhoff PM, Deray MJ, Rosengren S, Roeder ER, Enciso VB, Chinault AC, Patel A, Kang SH, Shaw CA, Lupski JR, Cheung SW. Observation and Prediction of Recurrent Human Translocations Mediated by Interchromosomal NAHR. Genome Res. 2011 Jan;21(1):33-46.

 

El-Hattab AW, Skorupski JC, Hsieh MH, Breman AM, Patel A, Cheung SW, Craigen WJ. 2009. OEIS complex associated with chromosome 1p36 deletion: A case report and review. Am J Med Genet A. 152A:504–511.

 

Breman AM, Bi WM, Cheung SW. Prenatal diagnosis by array-based comparative genomic hybridization in the clinical laboratory setting. Journal of Peking University (Health Sciences) 2009 Aug 18;41(4):500-4.

 

Oshima J, Magner DB, Lee JA, Breman AM, Schmitt ES, White LD, Crowe CA, Merill M, Jayakar P, Rajadhyaksha A, Eng CM, Del Gaudio D. Regional Genomic instability predisposes  to complex dystrophin gene rearrangements. Hum Genet. 2009 Sep;126(3):411-23.

 

Wat MJ, Shchelochkov OA, Holder AM, Breman AM, Dagli A, Bacino C, Scaglia F, Zori RT, Cheung SW, Scott DA, Kang SH. Chromosome 8p23.1 deletions as a cause of complex congenital heart defects and diaphragmatic hernia. Am J Med Genet A. 2009 Aug;149A(8):1661-77.

 

Grimes BR, Steiner CM, Merfeld-Clauss S, Traktuev DO, Smith D, Reese A, Breman AM, Thurston VC, Vance GH, Johnstone BH, Slee RB, March KL. Interphase FISH demonstrates that human adipose stromal cells maintain a high level of genomic stability in long term culture. Stem Cells and Development. 2009 Jun;18(5):717-24.

 

Bi W, Breman AM, Venable SF, Eng PA, Sahoo T, Lu XY, Patel A, Beaudet AL, Cheung SW, White LD. Rapid prenatal diagnosis using uncultured amniocytes and oligonucleotide array CGH. Prenatal Diagnosis. 2008 Oct;28(10):943-9.

 

Liang Z, Breman AM, Grimes BR, Rosen ED. Identifying and genotyping transgene integration loci.

Transgenic Research (2008) 17:979-983.

 

Breman AM, Steiner CM, Slee RB, Grimes BR. Input DNA ratio determines copy number of the 33 kb Factor IX gene on de novo human artificial chromosomes. Molecular Therapy. 2008 Feb;16(2):315-23.

Titles & Appointments

  • Associate Professor of Clinical Medical & Molecular Genetics
  • Co-Director, IU Cytogenetics Laboratory
  • Education
    2007 PhD Indiana University
    2001 BS Purdue University
  • Professional Organizations
    American College of Medical Genetics and Genomics (ACMG)
    International Society for Prenatal Diagnosis
  • Board Certifications
    American Board of Medical Genetics and Genomics - Clinical Cytogenetics and Genomics*

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