12968-Breman, Amy

Amy M. Breman, PhD

Professor of Clinical Medical & Molecular Genetics

Division Director, IU Genetic Testing Laboratories

Phone
(317) 274-8044
Address
IB 354A
MMGE
IN
Indianapolis, IN

Bio

Dr. Amy Breman is a laboratory geneticist and Professor of Clinical Medical and Molecular Genetics at the Indiana University School of Medicine in Indianapolis. She earned her BS from Purdue University and her PhD in Medical and Molecular Genetics from IU School of Medicine. Dr. Breman completed her ABMGG fellowship in Clinical Cytogenetics at Baylor College of Medicine in Houston, Texas, where she went on to serve as a  Cytogenetics lab director at Baylor Genetics laboratories. During her time there, she advanced to become Division Director of the Chromosomal Microarray Laboratory and Training Director for the ABMGG fellowship program in Cytogenetics.

In 2018, Dr. Breman returned to her home state of Indiana to join the IU Genetic Testing Laboratories as Co-Director of the Cytogenetics Laboratory. Since then, she has played a key role in expanding access to advanced diagnostic testing. In 2020, she completed additional training in the molecular genetics specialty and is now ABMGG board-certified in Clinical Molecular Genetics (Laboratory Genetics and Genomics).

Dr. Breman currently serves as Director of the Division of Diagnostic Genomics and Co-Director of multiple specialized laboratories, including the Cytogenetics and Pharmacogenomics Laboratories at IU Genetic Testing Labs.

Outside of her role at IU, Dr. Breman's service roles include being an Associate Editor for the journals Prenatal Diagnosis and Chromosome Research, serving as co-chair of the Opportunity, Access, and Engagement working group for the National Organization for Rare Disorders, and serving on various other committees for the American College of Medical Genetics and Genomics and the International Society for Prenatal Diagnosis. Her work spans clinical genetic testing, translational research, and laboratory leadership.

Key Publications

Springer AN, Alicea LA, Gafari Y, Smith TB, Lynch S, Breman AM, Hodge JC, Pratt VM, Powell NR, Kreutz RP, Kobold DP, Eadon MT, Tillman EM, Shugg T, Skaar TC. Evaluation of CYP2C19 Clinical Decision Support Alerts to Guide P2Y12 Inhibitor Prescribing. Clin Pharmacol Ther. 2025 Aug;118(2):470-479. 

Liaqat K, Treat K, Mantcheva L, McLaughlin A, Breman A, McPheron M, Conboy E, Vetrini F. Research-Based Whole Genome Sequencing Identifies Biallelic Loss of Function Variants in DOCK3 Gene Causing DOCK3-Related Disorder: The End of a Diagnostic Journey for This Family. Clin Genet. 2025 Jul;108(1):109-111. 

Lindstrom A, Breman A, Fitzgerald-Butt S, Helvaty LR, Ware SM, Helm BM. Evaluating first-line genetic testing strategies for inpatients with congenital heart defects. J Genet Couns. 2025 Jun;34(3):e70073.

Shugg T, Tillman EM, Breman AM, Hodge JC, McDonald CA, Ly RC, Rowe EJ, Osei W, Smith TB, Schwartz PH, Callaghan JT, Pratt VM, Lynch S, Eadon MT, Skaar TC. Development of a Multifaceted Program for Pharmacogenetics Adoption at an Academic Medical Center: Practical Considerations and Lessons Learned. Clin Pharmacol Ther. 2024 Oct;116(4):914-931.

Bellair M, Amaral E, Ouren M, Roark C, Kim J, O'Connor A, Soriano A, Schindler ML, Wapner RJ, Stone JL, Tavella N, Merriam A, Perley L, Breman AM, Beaudet AL. Noninvasive single-cell-based prenatal genetic testing: A proof of concept clinical study. Prenat Diagn. 2024 Mar;44(3):304-316. 

Ansari M, Faour KNW, Shimamura A, Grimes G, Kao EM, Denhoff ER, Blatnik A, Ben-Isvy D, Wang L, Helm BM, Firth H, Breman AM, Bijlsma EK, Iwata-Otsubo A, de Ravel TJL, Fusaro V, Fryer A, Nykamp K, Stühn LG, Haack TB, Korenke GC, Constantinou P, Bujakowska KM, Low KJ, Place E, Humberson J, Napier MP, Hoffman J, Juusola J, Deardorff MA, Shao W, Rockowitz S, Krantz I, Kaur M, Raible S, Kliesch S, Singer-Berk M, Groopman E, DiTroia S, Ballal S, Srivastava S, Rothfelder K, Biskup S, Rzasa J, Kerkhof J, McConkey H, O'Donnell-Luria A, Sadikovic B, Hilton S, Banka S, Tüttelmann F, Conrad D, Talkowski ME, FitzPatrick DR, Boone PM. Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features. HGG Adv. 2024 Apr 11;5(2):100273.

Shugg T, Ly RC, Osei W, Rowe EJ, Granfield CA, Lynnes TC, Medeiros EB, Hodge JC, Breman AM, Schneider BP, Sahinalp SC, Numanagic I, Salisbury BA, Bray SM, Ratcliff R, Skaar TC. Computational pharmacogenotype extraction from clinical next-generation sequencing. Front Oncol. 2023 Jul 4;13:1199741. 

Otsubo, A., Klee, V., Ahmad, A., Walsh, L., Breman, A. M. (2022). 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. Clinical Case Reports. 10(11):e6535.

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.

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.

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. 2022 Apr;31(2):479-488. PMID: 34570930.

Zhuo X, Wang Q, Vossaert L, Salman R, Kim A, Van den Veyver I, Breman A, Beaudet A. Use of amplicon-based sequencing for testing fetal identity and monogenic traits with Single Circulating Trophoblast (SCT) as one form of cell-based NIPT. PLoS One. 2021 Apr 15;16(4). PMID: 33857205.

Arya P, Hodge J, Matlock P, Vance G, Breman A. Two patients with complex rearrangements suggestive of germline chromoanagenesis. Cytogenet Genome Res. 2020;160(11-12):671-679. PMID: 33535208.

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

Yuan B, Wang L, Liu P, Shaw C, Dai H, Cooper L, Zhu W, Anderson SA, Meng L, Wang X, Wang Y, Xia F, Xiao R, Braxton A, Peacock S, Schmitt E, Ward PA, Vetrini F, He W, Chiang T, Muzny D, Gibbs RA, Beaudet AL, Breman AM, Smith J, Cheung SW, Bacino CA, Eng CM, Yang Y, Lupski JR, Bi W. CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. Genet Med. 2020 Oct;22(10):1633-1641. PMID: 32576985

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. Genomics. 2020 Sep;112(5):2937-2941.

Yang N, Wu N, Dong S, Zhang L, Zhao Y, Chen W, Du R, Song C, Ren X, Liu J, Pehlivan D, Liu Z, Jia R, Wang C, Zhao S, Breman AM, Xue H, Sun H, Shen J, Zhang S, Posey JE, Xu H, Jin L, Zhang J, Liu P, Sanna-Cherchi S, Qiu G, Wu Z, Lupski JR, Zhang F. Human and Mouse Studies Establish TBX6 in Mendelian CAKUT and as a Potential Driver of Kidney Defects Associated With the 16p11.2 Microdeletion Syndrome. Kidney Int. 2020 Oct;98(4):1020-1030.

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.

Dharmadhikari AV, Ghosh R, Yuan B, Liu P, Dai H, Al Masri S, Scull J, Posey JE, Jiang AH, He W, Vetrini F, Braxton AA, Ward P, Chiang T, Qu C, Gu S, Shaw CA, Smith JL, Lalani S, Stankiewicz P, Cheung SW, Bacino CA, Patel A, Breman AM, Wang X, Meng L, Xiao R, Xia F, Muzny D, Gibbs RA, Beaudet AL, Eng CM, Lupski JR, Yang Y, Bi W. 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.

Castelluccio VJ, Vetrini F, Lynnes T, Jones J, Holloway L, Belonis A, Breman AM, Graham BH, Sapp K, Wilson T, Schwartz CE, 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. 

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. Nat Med. 2019 Mar;25(3):439-447. 

Vossaert, L., Wang, Q., Salman, R., McCombs, A. K., Patel, V., Qu, C., Mancini, M. A., Edwards, D. P., Malovannaya, A., Liu, P., Shaw, C. A., Levy, B., Wapner, R. J., Bi, W., Breman, A. M., Van den Veyver, I. B., Beaudet, A. L. (2019). Validation Studies for Single Circulating Trophoblast Genetic Testing as a Form of Noninvasive Prenatal Diagnosis. Am J Hum Genet, 105(6), 1262-1273.

Yuan, B., Neira, J., Pehlivan, D., Santiago-Sim, T., Song, X., Rosenfeld, J., Posey, J. E., Patel, V., Jin, W., Adam, M. P., Baple, E. L., Dean, J., Fong, C. T., Hickey, S. E., Hudgins, L., Leon, E., Madan-Khetarpal, S., Rawlins, L., Rustad, C. F., Stray-Pedersen, A., Tveten, K., Wenger, O., Diaz, J., Jenkins, L., Martin, L., McGuire, M., Pietryga, M., Ramsdell, L., Slattery, L., Abid, F., Bertuch, A. A., Grange, D., Immken, L., Schaaf, C. P., Van Esch, H., Bi, W., Cheung, S. W., Breman, A. M., Smith, J. L., Shaw, C., Crosby, A. H., Eng, C., Yang, Y., Lupski, J. R., Xiao, R., Liu, P. (2018). Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. Genet in Med, 21(3):663-675.

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.e11. 

Gu, S., Jernegan, M., Van den Veyver, I. B., Peacock, S., Smith, J., Breman, A. M. (2018). Chromosomal microarray analysis on uncultured chorionic villus sampling can be complicated by confined placental mosaicism for aneuploidy and microdeletions. Prenatal Diagnosis, 38(11), 858-865.

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