Genome-wide structural variant analysis identifies risk loci for non-Alzheimer’s dementias

Kaivola, Karri; Chia, Ruth; Ding, Jinhui; Rasheed, Memoona; Fujita, Masashi; Menon, Vilas; Walton, Ronald L.; Collins, Ryan L.; Billingsley, Kimberley; Brand, Harrison; Talkowski, Michael; Zhao, Xuefang; Dewan, Ramita; Stark, Ali; Ray, Anindita; Solaiman, Sultana; Alvarez Jerez, Pilar; Malik, Laksh; Dawson, Ted M.; Rosenthal, Liana S.; Albert, Marilyn S.; Pletnikova, Olga; Troncoso, Juan C.; Masellis, Mario; Keith, Julia; Black, Sandra E.; Ferrucci, Luigi; Resnick, Susan M.; Tanaka, Toshiko; Topol, Eric; Torkamani, Ali; Tienari, Pentti; Foroud, Tatiana M.; Ghetti, Bernardino; Landers, John E.; Ryten, Mina; Morris, Huw R.; Hardy, John A.; Mazzini, Letizia; D'Alfonso, Sandra; Moglia, Cristina; Calvo, Andrea; Serrano, Geidy E.; Beach, Thomas G.; Ferman, Tanis; Graff-Radford, Neill R.; Boeve, Bradley F.; Wszolek, Zbigniew K.; Dickson, Dennis W.; Chiò, Adriano; Bennett, David A.; De Jager, Philip L.; Ross, Owen A.; Dalgard, Clifton L.; Gibbs, J. Raphael; Traynor, Bryan J.; Scholz, Sonja W.; Soltis, Anthony R.; Viollet, Coralie; Sukumar, Gauthaman; Alba, Camille; Lott, Nathaniel; McGrath Martinez, Elisa; Tuck, Meila; Singh, Jatinder; Bacikova, Dagmar; Zhang, Xijun; Hupalo, Daniel N.; Adeleye, Adelani; Wilkerson, Matthew D.; Pollard, Harvey B.; Dalgard, Clifton L.; Black, Sandra E.; Gan-Or, Ziv; Keith, Julia; Masellis, Mario; Rogaeva, Ekaterina; Brice, Alexis; Lesage, Suzanne; Xiromerisiou, Georgia; Calvo, Andrea; Canosa, Antonio; Chio, Adriano; Logroscino, Giancarlo; Mora, Gabriele; KRÜGER, Rejko; MAY, Patrick; Alcolea, Daniel; Clarimon, Jordi; Fortea, Juan; Gonzalez-Aramburu, Isabel; Infante, Jon; Lage, Carmen; Lleó, Alberto; Pastor, Pau; Sanchez-Juan, Pascual; Brett, Francesca; Aarsland, Dag; Al-Sarraj, Safa; Attems, Johannes; Gentleman, Steve; Hardy, John A.; Hodges, Angela K.; Love, Seth; McKeith, Ian G.; Morris, Christopher M.; Morris, Huw R.; Palmer, Laura; Pickering-Brown, Stuart; Ryten, Mina; Thomas, Alan J.; Troakes, Claire; Albert, Marilyn S.; Barrett, Matthew J.; Beach, Thomas G.; Bekris, Lynn M.; Bennett, David A.; Boeve, Bradley F.; Dalgard, Clifton L.; Dawson, Ted M.; Dickson, Dennis W.; Faber, Kelley; Ferman, Tanis; Ferrucci, Luigi; Flanagan, Margaret E.; Foroud, Tatiana M.; Ghetti, Bernardino; Gibbs, J. Raphael; Goate, Alison; Goldstein, David S.; Graff-Radford, Neill R.; Kaufmann, Horacio; Kukull, Walter A.; Leverenz, James B.; Lopez, Grisel; Mao, Qinwen; Masliah, Eliezer; Monuki, Edwin; Newell, Kathy L.; Palma, Jose-Alberto; Perkins, Matthew; Pletnikova, Olga; Renton, Alan E.; Resnick, Susan M.; Rosenthal, Liana S.; Ross, Owen A.; Scherzer, Clemens R.; Serrano, Geidy E.; Shakkottai, Vikram G.; Sidransky, Ellen; Tanaka, Toshiko; Tayebi, Nahid; Topol, Eric; Torkamani, Ali; Troncoso, Juan C.; Woltjer, Randy; Wszolek, Zbigniew K.; Scholz, Sonja W.; Baloh, Robert H.; Bowser, Robert; Brice, Alexis; Broach, James; Camu, William; Chiò, Adriano; Cooper-Knock, John; Drepper, Carsten; Drory, Vivian E.; Dunckley, Travis L.; Feldman, Eva; Fratta, Pietro; Gerhard, Glenn; Gibson, Summer B.; Glass, Jonathan D.; Hardy, John A.; Harms, Matthew B.; Heiman-Patterson, Terry D.; Jansson, Lilja; Kirby, Janine; Kwan, Justin; Laaksovirta, Hannu; Landers, John E.; Landi, Francesco; Le Ber, Isabelle; Lumbroso, Serge; MacGowan, Daniel J. L.; Maragakis, Nicholas J.; Mouzat, Kevin; Myllykangas, Liisa; Orrell, Richard W.; Ostrow, Lyle W.; Pamphlett, Roger; Pioro, Erik; Pulst, Stefan M.; Ravits, John M.; Robberecht, Wim; Rogaeva, Ekaterina; Rothstein, Jeffrey D.; Sendtner, Michael; Shaw, Pamela J.; Sidle, Katie C.; Simmons, Zachary; Stein, Thor; Stone, David J.; Tienari, Pentti J.; Traynor, Bryan J.; Troncoso, Juan C.; Valori, Miko; Van Damme, Philip; Van Deerlin, Vivianna M.; Van Den Bosch, Ludo; Zinman, Lorne

doi:10.1016/j.xgen.2023.100316

Download

Article (Scientific journals)

Genome-wide structural variant analysis identifies risk loci for non-Alzheimer’s dementias

Kaivola, Karri; Chia, Ruth; Ding, Jinhui et al.

2023 • In Cell Genomics, p. 100316

Peer Reviewed verified by ORBi

Permalink
https://hdl.handle.net/10993/55292

DOI
10.1016/j.xgen.2023.100316

Files (1)Send to Details Statistics Bibliography Similar publications

Files

Full Text

Kaivola2023.CellGenomics.pdf

Publisher postprint (4.19 MB)

Download

All documents in ORBilu are protected by a user license.

Send to

RIS BibTex APA Chicago Permalink X Linkedin

Details

Keywords :

Structural variants; Non-Alzheimer dementia; Lewy body dementia; frontotemporal dementia; amyotrophic lateral sclerosis

Abstract :

[en] We characterized the role of structural variants, a largely unexplored type of genetic variation, in two non-Alzheimer’s dementias, namely Lewy body dementia (LBD) and frontotemporal dementia (FTD)/amyotrophic lateral sclerosis (ALS). To do this, we applied an advanced structural variant calling pipeline (GATK-SV) to short-read whole-genome sequence data from 5,213 European-ancestry cases and 4,132 controls. We discovered, replicated, and validated a deletion in TPCN1 as a novel risk locus for LBD and detected the known structural variants at the C9orf72 and MAPT loci as associated with FTD/ALS. We also identified rare pathogenic structural variants in both LBD and FTD/ALS. Finally, we assembled a catalog of structural variants that can be mined for new insights into the pathogenesis of these understudied forms of dementia.

Research center :

- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
- Luxembourg Centre for Systems Biomedicine (LCSB): Clinical & Experimental Neuroscience (Krüger Group)
LIH - Luxembourg Institute of Health

Disciplines :

Neurology
Genetics & genetic processes

Author, co-author :

Kaivola, Karri

Chia, Ruth

Ding, Jinhui

Rasheed, Memoona

Fujita, Masashi

Menon, Vilas

Walton, Ronald L.

Collins, Ryan L.

Billingsley, Kimberley

Brand, Harrison

More authors (201 more)

External co-authors :

yes

Language :

English

Title :

Genome-wide structural variant analysis identifies risk loci for non-Alzheimer’s dementias

Publication date :

04 May 2023

Journal title :

Cell Genomics

ISSN :

2666-979X

Publisher :

Elsevier, New York, United States - New York

Pages :

100316

Peer reviewed :

Peer Reviewed verified by ORBi

Focus Area :

Systems Biomedicine

Additional URL :

https://linkinghub.elsevier.com/retrieve/pii/S2666979X23000848

FnR Project :

FNR11264123 - Ncer-pd, 2015 (01/01/2015-30/11/2020) - Rejko Krüger

Funders :

FNR - Fonds National de la Recherche

Available on ORBilu :

since 07 June 2023

Statistics

Number of views

91 (1 by Unilu)

Number of downloads

50 (0 by Unilu)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

OpenAlex citations

Bibliography

Ho, S.S., Urban, A.E., Mills, R.E., Structural variation in the sequencing era. Nat. Rev. Genet. 21 (2020), 171–189, 10.1038/s41576-019-0180-9.
Wheeler, D.A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y.J., Makhijani, V., Roth, G.T., et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452 (2008), 872–876, 10.1038/nature06884.
Blauwendraat, C., Pletnikova, O., Geiger, J.T., Murphy, N.A., Abramzon, Y., Rudow, G., Mamais, A., Sabir, M.S., Crain, B., Ahmed, S., et al. Genetic analysis of neurodegenerative diseases in a pathology cohort. Neurobiol. Aging, 76, 2019, 10.1016/j.neurobiolaging.2018.11.007 214.e1–214214.e9.
Guyant-Marechal, I., Berger, E., Laquerrière, A., Rovelet-Lecrux, A., Viennet, G., Frebourg, T., Rumbach, L., Campion, D., Hannequin, D., Intrafamilial diversity of phenotype associated with app duplication. Neurology 71 (2008), 1925–1926, 10.1212/01.wnl.0000339400.64213.56.
Farrer, M., Kachergus, J., Forno, L., Lincoln, S., Wang, D.S., Hulihan, M., Maraganore, D., Gwinn-Hardy, K., Wszolek, Z., Dickson, D., Langston, J.W., Comparison of kindreds with parkinsonism and alpha-synuclein genomic multiplications. Ann. Neurol. 55 (2004), 174–179, 10.1002/ana.10846.
Obi, T., Nishioka, K., Ross, O.A., Terada, T., Yamazaki, K., Sugiura, A., Takanashi, M., Mizoguchi, K., Mori, H., Mizuno, Y., Hattori, N., Clinicopathologic study of a SNCA gene duplication patient with Parkinson disease and dementia. Neurology 70 (2008), 238–241, 10.1212/01.wnl.0000299387.59159.db.
Toffoli, M., Chen, X., Sedlazeck, F.J., Lee, C.Y., Mullin, S., Higgins, A., Koletsi, S., Garcia-Segura, M.E., Sammler, E., Scholz, S.W., et al. Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson's disease-associated GBA gene. Commun. Biol., 5, 2022, 670, 10.1038/s42003-022-03610-7.
DeJesus-Hernandez, M., Mackenzie, I.R., Boeve, B.F., Boxer, A.L., Baker, M., Rutherford, N.J., Nicholson, A.M., Finch, N.A., Flynn, H., Adamson, J., et al. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 72 (2011), 245–256, 10.1016/j.neuron.2011.09.011.
Majounie, E., Renton, A.E., Mok, K., Dopper, E.G.P., Waite, A., Rollinson, S., Chiò, A., Restagno, G., Nicolaou, N., Simon-Sanchez, J., et al. Frequency of the C9orf72 hexanucleotide repeat expansion in patients with amyotrophic lateral sclerosis and frontotemporal dementia: a cross-sectional study. Lancet Neurol. 11 (2012), 323–330, 10.1016/S1474-4422(12)70043-1.
Renton, A.E., Majounie, E., Waite, A., Simón-Sánchez, J., Rollinson, S., Gibbs, J.R., Schymick, J.C., Laaksovirta, H., van Swieten, J.C., Myllykangas, L., et al. A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron 72 (2011), 257–268, 10.1016/j.neuron.2011.09.010.
Abel, H.J., Larson, D.E., Regier, A.A., Chiang, C., Das, I., Kanchi, K.L., Layer, R.M., Neale, B.M., Salerno, W.J., Reeves, C., et al. Mapping and characterization of structural variation in 17,795 human genomes. Nature 583 (2020), 83–89, 10.1038/s41586-020-2371-0.
Chia, R., Sabir, M.S., Bandres-Ciga, S., Saez-Atienzar, S., Reynolds, R.H., Gustavsson, E., Walton, R.L., Ahmed, S., Viollet, C., Ding, J., et al. Genome sequencing analysis identifies new loci associated with Lewy body dementia and provides insights into its genetic architecture. Nat. Genet. 53 (2021), 294–303, 10.1038/s41588-021-00785-3.
Dewan, R., Chia, R., Ding, J., Hickman, R.A., Stein, T.D., Abramzon, Y., Ahmed, S., Sabir, M.S., Portley, M.K., Tucci, A., et al. Pathogenic huntingtin repeat expansions in patients with frontotemporal dementia and amyotrophic lateral sclerosis. Neuron 109 (2021), 448–460.e4, 10.1016/j.neuron.2020.11.005.
Jakobsson, M., Scholz, S.W., Scheet, P., Gibbs, J.R., VanLiere, J.M., Fung, H.C., Szpiech, Z.A., Degnan, J.H., Wang, K., Guerreiro, R., et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451 (2008), 998–1003, 10.1038/nature06742.
Li, Y., Roberts, N.D., Wala, J.A., Shapira, O., Schumacher, S.E., Kumar, K., Khurana, E., Waszak, S., Korbel, J.O., Haber, J.E., et al. Patterns of somatic structural variation in human cancer genomes. Nature 578 (2020), 112–121, 10.1038/s41586-019-1913-9.
Sudmant, P.H., Rausch, T., Gardner, E.J., Handsaker, R.E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Fritz, M.H.Y., et al. An integrated map of structural variation in 2,504 human genomes. Nature 526 (2015), 75–81, 10.1038/nature15394.
English, A.C., Menon, V.K., Gibbs, R.A., Metcalf, G.A., Sedlazeck, F.J., Truvari: refined structural variant comparison preserves allelic diversity. Preprint at bioRxiv, 2022, 10.1101/2022.02.21.481353.
Byrska-Bishop, M., Evani, U.S., Zhao, X., Basile, A.O., Abel, H.J., Regier, A.A., Corvelo, A., Clarke, W.E., Musunuri, R., Nagulapalli, K., et al. High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios. Cell 185 (2022), 3426–3440.e19, 10.1016/j.cell.2022.08.004.
Vialle, R.A., de Paiva Lopes, K., Bennett, D.A., Crary, J.F., Raj, T., Integrating whole-genome sequencing with multi-omic data reveals the impact of structural variants on gene regulation in the human brain. Nat. Neurosci. 25 (2022), 504–514, 10.1038/s41593-022-01031-7.
Billingsley, K.J., Ding, J., Jerez, P.A., Illarianova, A., Grenn, F.P., Makarious, M.B., Moore, A., Vitale, D., Reed, X., Hernandez, D., et al. Genome-wide analysis of structural variants in Parkinson's disease using short-read sequencing data. BioRxiv https://doi.org/10.1101/2022.08.22.504867, 2022.
Hutton, M., Lendon, C.L., Rizzu, P., Baker, M., Froelich, S., Houlden, H., Pickering-Brown, S., Chakraverty, S., Isaacs, A., Grover, A., et al. Association of missense and 5’-splice-site mutations in tau with the inherited dementia FTDP-17. Nature 393 (1998), 702–705, 10.1038/31508.
Bellenguez, C., Küçükali, F., Jansen, I.E., Kleineidam, L., Moreno-Grau, S., Amin, N., Naj, A.C., Campos-Martin, R., Grenier-Boley, B., Andrade, V., et al. New insights into the genetic etiology of Alzheimer's disease and related dementias. Nat. Genet. 54 (2022), 412–436, 10.1038/s41588-022-01024-z.
Nalls, M.A., Blauwendraat, C., Vallerga, C.L., Heilbron, K., Bandres-Ciga, S., Chang, D., Tan, M., Kia, D.A., Noyce, A.J., Xue, A., et al. Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies. Lancet Neurol. 18 (2019), 1091–1102, 10.1016/S1474-4422(19)30320-5.
GTEx Consortium. The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369 (2020), 1318–1330, 10.1126/science.aaz1776.
Eraslan, G., Drokhlyansky, E., Anand, S., Fiskin, E., Subramanian, A., Slyper, M., Wang, J., Van Wittenberghe, N., Rouhana, J.M., Waldman, J., et al. Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Science, 376, 2022, eabl4290, 10.1126/science.abl4290.
Fujita, M., Gao, Z., Zeng, L., McCabe, C., White, C.C., Ng, B., Green, G.S., Rozenblatt-Rosen, O., Phillips, D., Amir-Zilberstein, L., et al. Cell-subtype specific effects of genetic variation in the aging and Alzheimer cortex. bioRxiv, 2022, 10.1101/2022.11.07.515446.
Grossman, M., Primary progressive aphasia: clinicopathological correlations. Nat. Rev. Neurol. 6 (2010), 88–97, 10.1038/nrneurol.2009.216.
Rajput, A., Dickson, D.W., Robinson, C.A., Ross, O.A., Dächsel, J.C., Lincoln, S.J., Cobb, S.A., Rajput, M.L., Farrer, M.J., Parkinsonism, Lrrk2 G2019S, and tau neuropathology. Neurology 67 (2006), 1506–1508, 10.1212/01.wnl.0000240220.33950.0c.
Bannwarth, S., Ait-El-Mkadem, S., Chaussenot, A., Genin, E.C., Lacas-Gervais, S., Fragaki, K., Berg-Alonso, L., Kageyama, Y., Serre, V., Moore, D.G., et al. A mitochondrial origin for frontotemporal dementia and amyotrophic lateral sclerosis through CHCHD10 involvement. Brain 137 (2014), 2329–2345, 10.1093/brain/awu138.
Dols-Icardo, O., Nebot, I., Gorostidi, A., Ortega-Cubero, S., Hernández, I., Rojas-García, R., García-Redondo, A., Povedano, M., Lladó, A., Álvarez, V., et al. Analysis of the CHCHD10 gene in patients with frontotemporal dementia and amyotrophic lateral sclerosis from Spain. Brain, 138, 2015, e400, 10.1093/brain/awv175.
Müller, K., Andersen, P.M., Hübers, A., Marroquin, N., Volk, A.E., Danzer, K.M., Meitinger, T., Ludolph, A.C., Strom, T.M., Weishaupt, J.H., Two novel mutations in conserved codons indicate that CHCHD10 is a gene associated with motor neuron disease. Brain, 137, 2014, e309, 10.1093/brain/awu227.
Woo, J.A.A., Liu, T., Trotter, C., Fang, C.C., De Narvaez, E., LePochat, P., Maslar, D., Bukhari, A., Zhao, X., Deonarine, A., et al. Loss of function CHCHD10 mutations in cytoplasmic TDP-43 accumulation and synaptic integrity. Nat. Commun., 8, 2017, 15558, 10.1038/ncomms15558.
Chow, C.Y., Landers, J.E., Bergren, S.K., Sapp, P.C., Grant, A.E., Jones, J.M., Everett, L., Lenk, G.M., McKenna-Yasek, D.M., Weisman, L.S., et al. Deleterious variants of FIG4, a phosphoinositide phosphatase, in patients with ALS. Am. J. Hum. Genet. 84 (2009), 85–88, 10.1016/j.ajhg.2008.12.010.
Ishibashi, K., Suzuki, M., Imai, M., Molecular cloning of a novel form (two-repeat) protein related to voltage-gated sodium and calcium channels. Biochem. Biophys. Res. Commun. 270 (2000), 370–376, 10.1006/bbrc.2000.2435.
Cang, C., Bekele, B., Ren, D., The voltage-gated sodium channel TPC1 confers endolysosomal excitability. Nat. Chem. Biol. 10 (2014), 463–469, 10.1038/nchembio.1522.
She, J., Guo, J., Chen, Q., Zeng, W., Jiang, Y., Bai, X.C., Structural insights into the voltage and phospholipid activation of the mammalian TPC1 channel. Nature 556 (2018), 130–134, 10.1038/nature26139.
Wang, X., Zhang, X., Dong, X.P., Samie, M., Li, X., Cheng, X., Goschka, A., Shen, D., Zhou, Y., Harlow, J., et al. TPC proteins are phosphoinositide- activated sodium-selective ion channels in endosomes and lysosomes. Cell 151 (2012), 372–383, 10.1016/j.cell.2012.08.036.
Foster, W.J., Taylor, H.B.C., Padamsey, Z., Jeans, A.F., Galione, A., Emptage, N.J., Hippocampal mGluR1-dependent long-term potentiation requires NAADP-mediated acidic store Ca(2+) signaling. Sci. Signal., 11, 2018, eaat9093, 10.1126/scisignal.aat9093.
Mallmann, R.T., Klugbauer, N., Genetic inactivation of two-pore channel 1 impairs spatial learning and memory. Behav. Genet. 50 (2020), 401–410, 10.1007/s10519-020-10011-1.
Neely Kayala, K.M., Dickinson, G.D., Minassian, A., Walls, K.C., Green, K.N., Laferla, F.M., Presenilin-null cells have altered two-pore calcium channel expression and lysosomal calcium: implications for lysosomal function. Brain Res. 1489 (2012), 8–16, 10.1016/j.brainres.2012.10.036.
Wacker, S.A., Alvarado, C., von Wichert, G., Knippschild, U., Wiedenmann, J., Clauss, K., Nienhaus, G.U., Hameister, H., Baumann, B., Borggrefe, T., et al. RITA, a novel modulator of Notch signalling, acts via nuclear export of RBP-J. EMBO J. 30 (2011), 43–56, 10.1038/emboj.2010.289.
Fuchs, J., Nilsson, C., Kachergus, J., Munz, M., Larsson, E.M., Schüle, B., Langston, J.W., Middleton, F.A., Ross, O.A., Hulihan, M., et al. Phenotypic variation in a large Swedish pedigree due to SNCA duplication and triplication. Neurology 68 (2007), 916–922, 10.1212/01.wnl.0000254458.17630.c5.
Pottier, C., Bieniek, K.F., Finch, N., van de Vorst, M., Baker, M., Perkersen, R., Brown, P., Ravenscroft, T., van Blitterswijk, M., Nicholson, A.M., et al. Whole-genome sequencing reveals important role for TBK1 and OPTN mutations in frontotemporal lobar degeneration without motor neuron disease. Acta Neuropathol. 130 (2015), 77–92, 10.1007/s00401-015-1436-x.
Iida, A., Hosono, N., Sano, M., Kamei, T., Oshima, S., Tokuda, T., Nakajima, M., Kubo, M., Nakamura, Y., Ikegawa, S., Novel deletion mutations of OPTN in amyotrophic lateral sclerosis in Japanese. Neurobiol. Aging 33 (2012), 1843.e19–1843.e24, 10.1016/j.neurobiolaging.2011.12.037.
Osawa, T., Mizuno, Y., Fujita, Y., Takatama, M., Nakazato, Y., Okamoto, K., Optineurin in neurodegenerative diseases. Neuropathology 31 (2011), 569–574, 10.1111/j.1440-1789.2011.01199.x.
Collins, R.L., Brand, H., Karczewski, K.J., Zhao, X., Alföldi, J., Francioli, L.C., Khera, A.V., Lowther, C., Gauthier, L.D., Wang, H., et al. A structural variation reference for medical and population genetics. Nature 581 (2020), 444–451, 10.1038/s41586-020-2287-8.
Chen, X., Schulz-Trieglaff, O., Shaw, R., Barnes, B., Schlesinger, F., Källberg, M., Cox, A.J., Kruglyak, S., Saunders, C.T., Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32 (2016), 1220–1222, 10.1093/bioinformatics/btv710.
Li, H., Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34 (2018), 3094–3100, 10.1093/bioinformatics/bty191.
Li, H., New strategies to improve minimap2 alignment accuracy. Bioinformatics 37 (2021), 4572–4574, 10.1093/bioinformatics/btab705.
Sedlazeck, F.J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., von Haeseler, A., Schatz, M.C., Accurate detection of complex structural variations using single-molecule sequencing. Nat. Methods 15 (2018), 461–468, 10.1038/s41592-018-0001-7.
Chang, C.C., Chow, C.C., Tellier, L.C., Vattikuti, S., Purcell, S.M., Lee, J.J., Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience, 4, 2015, 7, 10.1186/s13742-015-0047-8.
Abraham, G., Qiu, Y., Inouye, M., FlashPCA2: principal component analysis of Biobank-scale genotype datasets. Bioinformatics 33 (2017), 2776–2778, 10.1093/bioinformatics/btx299.
Danecek, P., Bonfield, J.K., Liddle, J., Marshall, J., Ohan, V., Pollard, M.O., Whitwham, A., Keane, T., McCarthy, S.A., Davies, R.M., Li, H., Twelve years of SAMtools and BCFtools. GigaScience, 10, 2021, giab008, 10.1093/gigascience/giab008.
Robinson, J.T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G., Mesirov, J.P., Integrative genomics viewer. Nat. Biotechnol. 29 (2011), 24–26, 10.1038/nbt.1754.
Willer, C.J., Li, Y., Abecasis, G.R., METAL: fast and efficient meta-analysis of genomewide association scans. Bioinformatics 26 (2010), 2190–2191, 10.1093/bioinformatics/btq340.
Kleinert, P., Kircher, M., A framework to score the effects of structural variants in health and disease. Genome Res. 32 (2022), 766–777, 10.1101/gr.275995.121.
Boughton, A.P., Welch, R.P., Flickinger, M., VandeHaar, P., Taliun, D., Abecasis, G.R., Boehnke, M., LocusZoom.js: interactive and embeddable visualization of genetic association study results. Bioinformatics 37 (2021), 3017–3018.
Belyeu, J.R., Chowdhury, M., Brown, J., Pedersen, B.S., Cormier, M.J., Quinlan, A.R., Layer, R.M., Samplot: a platform for structural variant visual validation and automated filtering. Genome Biol., 22, 2021, 161.
Emre, M., Aarsland, D., Brown, R., Burn, D.J., Duyckaerts, C., Mizuno, Y., Broe, G.A., Cummings, J., Dickson, D.W., Gauthier, S., et al. Clinical diagnostic criteria for dementia associated with Parkinson's disease. Mov. Disord. 22 (2007), 1689–1707, 10.1002/mds.21507 quiz 1837.
McKeith, I.G., Boeve, B.F., Dickson, D.W., Halliday, G., Taylor, J.P., Weintraub, D., Aarsland, D., Galvin, J., Attems, J., Ballard, C.G., et al. Diagnosis and management of dementia with Lewy bodies: fourth consensus report of the DLB Consortium. Neurology 89 (2017), 88–100, 10.1212/WNL.0000000000004058.
Neary, D., Snowden, J.S., Gustafson, L., Passant, U., Stuss, D., Black, S., Freedman, M., Kertesz, A., Robert, P.H., Albert, M., et al. Frontotemporal lobar degeneration: a consensus on clinical diagnostic criteria. Neurology 51 (1998), 1546–1554, 10.1212/wnl.51.6.1546.
Höglinger, G.U., Respondek, G., Stamelou, M., Kurz, C., Josephs, K.A., Lang, A.E., Mollenhauer, B., Müller, U., Nilsson, C., Whitwell, J.L., et al. Clinical diagnosis of progressive supranuclear palsy: the movement disorder society criteria. Mov. Disord. 32 (2017), 853–864, 10.1002/mds.26987.
Brooks, B.R., Miller, R.G., Swash, M., Munsat, T.L., World Federation of Neurology Research Group on Motor Neuron Diseases. El Escorial revisited: revised criteria for the diagnosis of amyotrophic lateral sclerosis. Amyotroph Lateral Scler. 1 (2000), 293–299, 10.1080/146608200300079536.
Erikson, G.A., Bodian, D.L., Rueda, M., Molparia, B., Scott, E.R., Scott-Van Zeeland, A.A., Topol, S.E., Wineinger, N.E., Niederhuber, J.E., Topol, E.J., Torkamani, A., Whole-genome sequencing of a healthy aging cohort. Cell 165 (2016), 1002–1011, 10.1016/j.cell.2016.03.022.
Werling, D.M., Brand, H., An, J.Y., Stone, M.R., Zhu, L., Glessner, J.T., Collins, R.L., Dong, S., Layer, R.M., Markenscoff-Papadimitriou, E., et al. An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nat. Genet. 50 (2018), 727–736, 10.1038/s41588-018-0107-y.
Gardner, E.J., Lam, V.K., Harris, D.N., Chuang, N.T., Scott, E.C., Pittard, W.S., Mills, R.E., Devine, S.E., 1000 Genomes Project Consortium. the mobile element locator tool (MELT): population-scale mobile element discovery and biology. Genome Res. 27 (2017), 1916–1929, 10.1101/gr.218032.116.
Kronenberg, Z.N., Osborne, E.J., Cone, K.R., Kennedy, B.J., Domyan, E.T., Shapiro, M.D., Elde, N.C., Yandell, M., Wham: identifying structural variants of biological consequence. PLoS Comput. Biol., 11, 2015, e1004572, 10.1371/journal.pcbi.1004572.
Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.A., Mitterecker, A., Bodenhofer, U., Hochreiter, S., cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate. Nucleic Acids Res., 40, 2012, e69, 10.1093/nar/gks003.
Van der Auwera, G.A., O'Connor, B.D., Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. 2020, O'Reilly Media.
Smolka, M., Paulin, L.F., Grochowski, C.M., Mahmoud, M., Behera, S., Gandhi, M., Hong, K., Pehlivan, D., Scholz, S.W., Carvalho, C.M.B., et al. Comprehensive structural variant detection: from mosaic to population-level. Preprint at bioRxiv, 2022, 10.1101/2022.04.04.487055.
Karolchik, D., Hinrichs, A.S., Furey, T.S., Roskin, K.M., Sugnet, C.W., Haussler, D., Kent, W.J., The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32 (2004), D493–D496, 10.1093/nar/gkh103.
Hahne, F., Ivanek, R., Visualizing genomic data using Gviz and bioconductor. Methods Mol. Biol. 1418 (2016), 335–351, 10.1007/978-1-4939-3578-9_16.
Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W.M. 3rd, Hao, Y., Stoeckius, M., Smibert, P., Satija, R., Comprehensive integration of single-cell data. Cell 177 (2019), 1888–1902.e21, 10.1016/j.cell.2019.05.031.
Shabalin, A.A., Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 28 (2012), 1353–1358, 10.1093/bioinformatics/bts163.