Junior Research Group Genome Informatics

Birte Kehr joined BIH in November 2016 to establish the Junior Research Group Genome Informatics. She and her team are developing computational approaches for the analysis of genome sequencing data with a focus on the detection of structural variation. Birte Kehr describes their work in a brief portrait:

Research focus

We develop algorithms for identifying genomic variation from sequencing data. Genomic variation is generally classified in small variants (SNVs and indels) and larger variants (structural variants), which can be identified through the analysis of modern sequencing data. While approaches for the extraction of small variants are becoming more standard, the identification of structural variants still poses many challenges.

We explore data types from the most recent technologies and make use of the magnitude of sequencing data available to improve our abilities to characterize structural variation. In particular, we develop and implement new computational tools using algorithmic approaches from the field of sequence analysis, in which we incorporate statistical models that account for the specific properties of the data.

How can patients benefit from your research one day?

Susceptibility to disease and response to medical treatment are influenced by variation in the genome. In order to understand the genetics of a patient, comprehensive and reliable catalogues of genomic variation are needed. Our research aims at improving the automated generation of such catalogues from genome sequencing data and thereby provides doctors with the information needed for more precise diagnoses and individual treatment decisions.

The most important thing for me is ...

... to deepen our understanding of genetic variation and its role in disease.

Team

Birte Kehr, Group Leader

Tim White, Postdoc, tim.white@bihealth.de
Sebastian Roskosch, PhD student, sebastian.roskosch@bihealth.de
Thomas Krannich, PhD student, thomas.krannich@bihealth.de

Prior to joining the BIH, Birte Kehr worked as a Research Scientist at deCODE genetics in Iceland. There she gained experience in working with large-scale genomic data and developed a particular interest in structural variation discovery for understanding human disease. She received her PhD from the Freie Universität Berlin within the International Max Planck Research School for Computational Biology and Scientific Computing in 2014. Her thesis addressed algorithms and data structures for multiple whole-genome alignment.https://www.bihealth.org/

Selected publications

Jónsson H, Sulem P, Kehr B, Kristmundsdottir S, Zink F, Hjartarson E, Hardarson MT, Hjorleifsson KE, Eggertsson HP, Gudjonsson SA, Ward LD, Arnadottir GA, Helgason EA, Helgason H, Gylfason A, Jonasdottir Ad, Jonasdottir As, Rafnar Th, Frigge M, Stacey SN, Magnusson OTh, Thorsteinsdottir U, Masson G, Kong A, Halldorsson BV, Helgason A, Gudbjartsson DF, Stefansson K (2017). Parental influence on human germline de novo mutations in 1,548 trios from Iceland. Nature, 549:519–522.

Kehr K, Helgadottir A, Melsted P, Jonsson H, Helgason H, Jonasdottir Ad, Jonasdottir As, Sigurdsson A, Gylfason A, Halldorsson GH, Kristmundsdottir S, Thorgeirsson G, Olafsson I, Holm H, Thorsteinsdottir U, Sulem P, Helgason A, Gudbjartsson DF, Halldorsson BV, Stefansson K (2017). Diversity in non-repetitive human sequences not found in the reference genome. Nat Genet, 49(4):588-593.

Haraldsdottir S, Rafnar Th, Frankel WL, Einarsdottir S, Sigurdsson A, Hampel H, Snaebjornsson P, Masson G, Weng D, Arngrimsson R, Kehr B, Yilmaz A, Haraldsson S, Sulem P, Stefansson T, Shields PG, Sigurdsson F, Bekaii-Saab T, Moller PH, Steinarsdottir M, Alexiusdottir K, Hitchins M, Pritchard CC, de la Chapelle A, Jonasson JG, Goldberg RM, Stefansson K (2017). Comprehensive population-wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2. Nat Commun, 8:14755.

Kehr B, Melsted P, Halldorsson BV (2016). PopIns: population-scale detection of novel sequence insertions. Bioinformatics, 32(7):961-967.

Halldorsson BV, Hardarson MT, Kehr B, Styrkarsdottir U, Gylfason A, Thorleifsson G, Zink F, Jonasdottir A, Jonasdottir A, Sulem P, Masson G, Thorsteinsdottir U, Helgason A, Kong A, Gudbjartsson DF, Stefansson K (2016). The rate of meiotic gene conversion varies by sex and age. Nat Genet, 48(11):1377-84.

Kehr B, Melsted P (2016). chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts. Bioinformatics, 32(14):2202-2204.

Stacey SN, Kehr B, Gudmundsson J, Zink F, Jonasdottir A, Gudjonsson SA, Sigurdsson A, Halldorsson BV, Agnarsson BA, Benediktsdottir KR, Aben KK, Vermeulen SH, Cremers RG, Panadero A, Helfand BT, Cooper PR, Donovan JL, Hamdy FC, Jinga V, Okamoto I, Jonasson JG, Tryggvadottir L, Johannsdottir H, Kristinsdottir AM, Masson G, Magnusson OT, Iordache PD, Helgason A, Helgason H, Sulem P, Gudbjartsson DF, Kong A, Jonsson E, Barkardottir RB, Einarsson GV, Rafnar T, Thorsteinsdottir U, Mates IN, Neal DE, Catalona WJ, Mayordomo JI, Kiemeney LA, Thorleifsson G, Stefansson K (2016). Insertion of an SVA-E retrotransposon into the CASP8 gene is associated with protection against prostate cancer. Hum Mol Genet 25(5):1008-18.