AH Andreas HalmanResearcher's profile
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Tandem-repeat disorders

Rare diseases

My work in rare diseases aims to improve the diagnosis of specific genetic mutations in people living with undiagnosed rare diseases.

Overview of the field & contribution

Overview

Short tandem repeat (STR) expansions cause more than 60 inherited disorders, most of which are neurological. Many can be challenging to detect and interpret using commonly available short-read sequencing data. My work has focused on developing methods to improve STR genotyping and making these analyses more accessible to researchers and clinicians.

Practical contribution

I have contributed to the evaluation and development of methods for STR analysis. I developed the STRipy software and online resources, including a curated database of known disease-causing STR loci. I have also developed a protocol for analysing known and novel STR loci from short-read sequencing data. Other co-authored tools include STRetch and REViewer for rare diseases and Toblerone for cancer research.

Published research

Recent publications

2023 Integrated multi-omics for rapid rare disease diagnosis on a national scale Lunke, S, Bouffler, S, Patel, C, Sandaradura, S, Wilson, M, Pinner, J, Hunter, M, Barnett, C, Wallis, M, Kamien, B, Tan, T, Freckmann, M, Chong, B, Phelan, D, Francis, D, Kassahn, K, Ha, T, Gao, S, Arts, P, Jackson, M, Scott, H, Eggers, S, Rowley, S, Boggs, K, Rakonjac, A, Brett, G, de Silva, M, Springer, A, Ward, M, Stallard, K, Simons, C, Conway, T, Halman, A, Van Bergen, N, Sikora, T, Semcesen, L, Stroud, D, Compton, A, Thorburn, D, Bell, K, Sadedin, S, North, K, Christodoulou, J, Stark, Z Nature Medicine 2023 Toblerone: detecting exon deletion events in cancer using RNA-seq Lonsdale, A, Halman, A, Brown, L, Kosasih, H, Ekert, P, Oshlack, A F1000Research 2022 REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats Dolzhenko, E, Weisburd, B, Ibañez, K, Rajan-Babu, I, Anyansi, C, Bennett, M, Billingsley, K, Carroll, A, Clamons, S, Danzi, M, Deshpande, V, Ding, J, Fazal, S, Halman, A, Jadhav, B, Qiu, Y, Richmond, P, Saunders, C, Scheffler, K, van Vugt, J, Zwamborn, R, Genomics England Research Consortium, Chong, S, Friedman, J, Tucci, A, Rehm, H, Eberle, M Genome Medicine 2022 STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data Halman, A, Dolzhenko, E, Oshlack, A Human Mutation 2020 Accuracy of short tandem repeats genotyping tools in whole exome sequencing data Halman, A, Oshlack, A F1000Research