12968-Breman, Amy

Amy M. Breman, PhD

Associate Professor of Clinical Medical & Molecular Genetics

Division Director, IU Genetic Testing Laboratories

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


Amy Breman, PhD, is an Associate Professor of Medical and Molecular Genetics, and Division Director of the Indiana University Genetic Testing Labs (IUGTL). Dr. Breman has a broad background in clinical genetic testing and translational research studies, having spent 10 years as a laboratory director at Baylor Genetics before joining Indiana University in 2018. In that capacity, Dr. Breman worked with Dr. Arthur Beaudet to develop a novel clinical approach to noninvasive prenatal diagnosis using circulating fetal cells.

In 2021, Dr. Breman completed her second ABMGG clinical laboratory fellowship and became board-certified in clinical molecular genetics. This allowed Dr. Breman to not only expand her clinical expertise in to molecular diagnostics, but also led to her involvement in several new clinical research studies, including development of genome sequencing processes for the Undiagnosed Rare Disease Clinic (URDC) and pharmacogenomic genotyping for the Personalized Perioperative Analgesia Platform (PPAP) for Cesarean Section study, among others.

As the current director of the division of diagnostic genomics, Dr. Breman's responsibilities include oversight of the lab’s efforts to uphold CLIA and CAP standards, including participation in QA/QC monitoring, laboratory inspections (both internal and external) and proficiency testing. Dr. Breman is 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.

Dr. Breman's solid clinical laboratory experience has allowed her to engage and provide guidance on a variety of multidisciplinary collaborative research studies, including the oversight of analytical and clinical validation requirements for implementation of new clinical testing methodologies.

Key Publications

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. doi: 10.1002/pd.6529. Epub 2024 Feb 27.PMID: 38411249

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. medRxiv [Preprint]. 2023 Sep 28:2023.09.27.23294269. doi: 10.1101/2023.09.27.23294269. PMID: 37808847; PMCID: PMC10557843.

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. - Cancer Genetics. Vol 13 – 2023. In Press.

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

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.

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