@article{2832c1a91cb6416b9a54c0d61ade4561,
title = "LUSTR: a new customizable tool for calling genome-wide germline and somatic short tandem repeat variants",
abstract = "Background: Short tandem repeats (STRs) are widely distributed across the human genome and are associated with numerous neurological disorders. However, the extent that STRs contribute to disease is likely under-estimated because of the challenges calling these variants in short read next generation sequencing data. Several computational tools have been developed for STR variant calling, but none fully address all of the complexities associated with this variant class. Results: Here we introduce LUSTR which is designed to address some of the challenges associated with STR variant calling by enabling more flexibility in defining STR loci, allowing for customizable modules to tailor analyses, and expanding the capability to call somatic and multiallelic STR variants. LUSTR is a user-friendly and easily customizable tool for targeted or unbiased genome-wide STR variant screening that can use either predefined or novel genome builds. Using both simulated and real data sets, we demonstrated that LUSTR accurately infers germline and somatic STR expansions in individuals with and without diseases. Conclusions: LUSTR offers a powerful and user-friendly approach that allows for the identification of STR variants and can facilitate more comprehensive studies evaluating the role of pathogenic STR variants across human diseases.",
keywords = "Bioinformatics, LUSTR, Short tandem repeats, Somatic, Variant calling tool kit",
author = "{Undiagnosed Diseases Network} and Jinfeng Lu and Camilo Toro and Adams, {David R.} and Moreno, {Cristiane Araujo Martins} and Lee, {Wan Ping} and Leung, {Yuk Yee} and Harms, {Mathew B.} and Badri Vardarajan and Heinzen, {Erin L.} and Acosta, {Maria T.} and Margaret Adam and Kosuke Izumi and Alvarez, {Raquel L.} and Justin Alvey and Laura Amendola and Ashley Andrews and Ashley, {Euan A.} and Bacino, {Carlos A.} and Guney Bademci and Ashok Balasubramanyam and Dustin Baldridge and Jim Bale and Michael Bamshad and Deborah Barbouth and Pinar Bayrak-Toydemir and Anita Beck and Beggs, {Alan H.} and Edward Behrens and Gill Bejerano and Bellen, {Hugo J.} and Jimmy Bennett and Beverly Berg-Rood and Bernstein, {Jonathan A.} and Berry, {Gerard T.} and Anna Bican and Stephanie Bivona and Elizabeth Blue and John Bohnsack and Devon Bonner and Lorenzo Botto and Brenna Boyd and Briere, {Lauren C.} and Gabrielle Brown and Burke, {Elizabeth A.} and Burrage, {Lindsay C.} and Butte, {Manish J.} and Peter Byers and Byrd, {William E.} and John Carey and Olveen Carrasquillo and Thomas Cassini and Chang, {Ta Chen Peter} and Sirisak Chanprasert and Chao, {Hsiao Tuan} and Ivan Chinn and Clark, {Gary D.} and Coakley, {Terra R.} and Cobban, {Laurel A.} and Cogan, {Joy D.} and Matthew Coggins and Cole, {F. Sessions} and Colley, {Heather A.} and Heidi Cope and Rosario Corona and Craigen, {William J.} and Crouse, {Andrew B.} and Michael Cunningham and Precilla D{\textquoteright}Souza and Hongzheng Dai and Surendra Dasari and Joie Davis and Dayal, {Jyoti G.} and Dell{\textquoteright}Angelica, {Esteban C.} and Patricia Dickson and Katrina Dipple and Daniel Doherty and Naghmeh Dorrani and Doss, {Argenia L.} and Douine, {Emilie D.} and Dawn Earl and Eckstein, {David J.} and Emrick, {Lisa T.} and Eng, {Christine M.} and Marni Falk and Fieg, {Elizabeth L.} and Fisher, {Paul G.} and Fogel, {Brent L.} and Irman Forghani and Gahl, {William A.} and Ian Glass and Bernadette Gochuico and Goddard, {Page C.} and Godfrey, {Rena A.} and Katie Golden-Grant and Alana Grajewski and Don Hadley and Sihoun Hahn and Halley, {Meghan C.} and Rizwan Hamid and Kelly Hassey and Nichole Hayes and Frances High and Anne Hing and Hisama, {Fuki M.} and Holm, {Ingrid A.} and Jason Hom and Martha Horike-Pyne and Alden Huang and Sarah Hutchison and Wendy Introne and Rosario Isasi and Kosuke Izumi and Fariha Jamal and Jarvik, {Gail P.} and Jeffrey Jarvik and Suman Jayadev and Orpa Jean-Marie and Vaidehi Jobanputra and Lefkothea Karaviti and Shamika Ketkar and Dana Kiley and Gonench Kilich and Kobren, {Shilpa N.} and Kohane, {Isaac S.} and Kohler, {Jennefer N.} and Susan Korrick and Mary Kozuira and Deborah Krakow and Krasnewich, {Donna M.} and Elijah Kravets and Lalani, {Seema R.} and Byron Lam and Christina Lam and Lanpher, {Brendan C.} and Lanza, {Ian R.} and Kimberly LeBlanc and Lee, {Brendan H.} and Roy Levitt and Lewis, {Richard A.} and Pengfei Liu and Liu, {Xue Zhong} and Nicola Longo and Loo, {Sandra K.} and Joseph Loscalzo and Maas, {Richard L.} and Macnamara, {Ellen F.} and MacRae, {Calum A.} and Maduro, {Valerie V.} and Maghiro, {Audrey Stephannie} and Rachel Mahoney and Malicdan, {May Christine V.} and Mamounas, {Laura A.} and Manolio, {Teri A.} and Rong Mao and Kenneth Maravilla and Ronit Marom and Gabor Marth and Martin, {Beth A.} and Martin, {Martin G.} and Mart{\'i}nez-Agosto, {Julian A.} and Shruti Marwaha and Jacob McCauley and Allyn McConkie-Rosell and McCray, {Alexa T.} and Elisabeth McGee and Heather Mefford and Merritt, {J. Lawrence} and Matthew Might and Ghayda Mirzaa and Eva Morava and Paolo Moretti and John Mulvihill and Mariko Nakano-Okuno and Nelson, {Stanley F.} and Newman, {John H.} and Nicholas, {Sarah K.} and Deborah Nickerson and Shirley Nieves-Rodriguez and Donna Novacic and Devin Oglesbee and Orengo, {James P.} and Laura Pace and Stephen Pak and Pallais, {J. Carl} and Palmer, {Christina G.S.} and Papp, {Jeanette C.} and Parker, {Neil H.} and Phillips, {John A.} and Posey, {Jennifer E.} and Lorraine Potocki and Swerdzewski, {Barbara N.Pusey} and Aaron Quinlan and Rao, {Deepak A.} and Anna Raper and Wendy Raskind and Genecee Renteria and Timothy Schedl and Jimann Shin and Lilianna Solnica-Krezel and Jennifer Wambach",
note = "Publisher Copyright: {\textcopyright} The Author(s) 2024.",
year = "2024",
month = dec,
doi = "10.1186/s12864-023-09935-9",
language = "English",
volume = "25",
journal = "BMC genomics",
issn = "1471-2164",
number = "1",
}