12968-Breman, Amy

Amy M. Breman, PhD

Associate Professor of Clinical Medical & Molecular Genetics

IB 354C
Indianapolis, IN


Amy Breman, PhD, is an Associate Professor in the Department of Medical and Molecular Genetics at IU School of Medicine. Dr. Breman earned her BS from Purdue University in 2001 and her PhD in Medical and Molecular Genetics from IUSM in 2007. In 2011, Dr. Breman completed her ABMGG fellowship in Clinical Cytogenetics at Baylor College of Medicine in Houston, Texas, and later became a laboratory director of cytogenetics at Baylor Genetics labs. During her 10 years with Baylor Genetics, she advanced to Division Director of the Chromosomal Microarray Laboratory and Training Director in Cytogenetics for the ABMGG fellowship program.

Dr. Breman returned to her home state of Indiana in 2018 to join the IU Genetic Testing Laboratories as a co-director of Cytogenetics. Since then she has completed a second ABMGG board certification in Clinical Molecular Genetics, and currently serves as a co-director of both the Pharmacogenomics and Cytogenetics Laboratories. Starting in 2023, Dr. Breman serves as Divison Director of the IU Genetic Testing Laboratories.

Key Publications

  1. Iwata-Otsubo A, Klee VH, Ahmad AA, Walsh LE, Breman AM. A 9.8 Mb deletion at 7q31.2q31.31 downstream of FOXP2 in an individual with speech and language impairment suggests a possible positional effect. Clin Case Rep. 2022 Nov 19. https://doi.org/10.1002/ccr3.6535
  2. Sikkink K, Delk P, Wetherill L, Breman A, Wesson M. Factors That Influence Genetic Counselors’ Participation in Research. J Genet Couns. 2022 Oct 10. PMID: 36210790.
  3. Badar SA, Breman AM, Christensen CK, Graham BH, Golomb MR. Girl-Boy Twins With Developmental Delay from 16p11.2 Triplication Due to Bi-Parental Inheritance From Two Parents with 16p11.2 Duplication. Cytogenet Genome Res. 2022;162(1-2):40-45. PMID: 35139523.
  4. Richardson B, Fitzgerald-Butt SM, Spoonamore KG, Wetherill L, Helm BM, Breman A. Management of Amended Variant Classification Laboratory Reports by Genetic Counselors in the United States and Canada: An Exploratory Study. J Genet Couns. 2021 Sep 27.
  5. Breman, A and Stankiewicz, P. Karyotyping as the First Genomic Approach. In: Gonzaga-Jauregui C, Lupski JR (Eds). Genomics of Rare Diseases: Understanding Disease Genetics Using Genomic Approaches. San Diego: Academic Press / Elsevier Inc., 2021: pp 17-31.
  6. Pettersson M, Grochowski C, Wincent J, Eisfeldt J, Breman A, Cheung SW, Krepischi A, Rosenberg C, Lupski J, Ottosson J, Lovmar L, Gacic J, Lundberg E, Nilsson D, Carvalho C, Lindstrand A.Cytogenetically visible inversions are formed by multiple molecular mechanisms. Human Mutation. September 9, 2020. PMID: 32906200
  7. Liu Q, Karolak JA, Grochowski CM, Wilson TA, Rosenfeld JA, Bacino CA, Lalani SR, Patel A, Breman A, Smith JL, Cheung SW, Lupski JR, Bi W, Stankiewicz P. Parental Somatic Mosaicism for CNV Deletions - A Need for More Sensitive and Precise Detection Methods in Clinical Diagnostics Settings. 2020 May 6;S0888-7543(20)30340-2.
  8. 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. 2020 Apr;63(4):103797.
  9. 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.
  10. 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 Genetic Testing as a Form of Noninvasive Prenatal Diagnosis. Am J Hum Genet. 2019 Dec 5;105(6):1262-1273.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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. 2018 Feb 22;172(5):924-936.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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. 2017 Feb 23;168(5):830-842.
  22. 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.
  23. Breman AM, Chow JC, U'Ren L, Normand EA, Qdaisat S, Zhao L, Henke DM, Chen R, Shaw CA, Jackson L, Yang Y, Vossaert L, Needham RH, Chang EJ, Campton D, Werbin JL, Seubert RC, Van den Veyver IB, Stilwell JL, Kaldjian EP, Beaudet AL. Evidence for feasibility of fetal trophoblastic cell-based noninvasive prenatal testing. Prenat Diagn. 2016 Nov;36(11):1009-1019.
  24. 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.
  25. 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.
  26. 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. 2013 Nov 7;503(7474):72-7.
  27. Dittwald P, Gambin T, Szafranski P, Li J, Amato S, Divon MY, Rodríguez Rojas LX, Elton LE, Scott DA, Schaaf CP, Torres-Martinez W, Stevens AK, Rosenfeld JA, Agadi S, Francis D, Kang SH, Breman A, Lalani SR, Bacino CA, Bi W, Milosavljevic A, Beaudet AL, Patel A, Shaw CA, Lupski JR, Gambin A, Cheung SW, Stankiewicz P. 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.
  28. 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.
  29. Amy Breman and Ankita Patel. Preparation of Chorionic Villus Samples for Metaphase Chromosome Analysis and Chromosomal Microarray Analysis. Current Protocols in Human Genetics3.1-8.3.9, October 2012. (Invited article)
  30. BremanA, 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.
  31. 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.
  32. 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 Genet2011 Oct;19(10):1110.
  33. 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.
  34. 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.
  35. 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.
  36. 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.

Titles & Appointments

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

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