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Hitz MP, Lemieux-Perreault LP, Marshall C, Feroz-Zada Y, Davies R, Yang SW, Lionel AC, D'Amours G, Lemyre E, Cullum R, Bigras JL, Thibeault M, Chetaille P, Montpetit A, Khairy P, Overduin B, Klaassen S, Hoodless P, Nemer M, Stewart AFR, Boerkoel C, Scherer SW, Richter A, Dubé MP, Andelfinger G. Rare copy number variants contribute to congenital left-sided heart disease. PLoS Genet 2012; 8:e1002903. [PMID: 22969434 PMCID: PMC3435243 DOI: 10.1371/journal.pgen.1002903] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 07/03/2012] [Indexed: 12/13/2022] Open
Abstract
Left-sided congenital heart disease (CHD) encompasses a spectrum of malformations that range from bicuspid aortic valve to hypoplastic left heart syndrome. It contributes significantly to infant mortality and has serious implications in adult cardiology. Although left-sided CHD is known to be highly heritable, the underlying genetic determinants are largely unidentified. In this study, we sought to determine the impact of structural genomic variation on left-sided CHD and compared multiplex families (464 individuals with 174 affecteds (37.5%) in 59 multiplex families and 8 trios) to 1,582 well-phenotyped controls. 73 unique inherited or de novo CNVs in 54 individuals were identified in the left-sided CHD cohort. After stringent filtering, our gene inventory reveals 25 new candidates for LS-CHD pathogenesis, such as SMC1A, MFAP4, and CTHRC1, and overlaps with several known syndromic loci. Conservative estimation examining the overlap of the prioritized gene content with CNVs present only in affected individuals in our cohort implies a strong effect for unique CNVs in at least 10% of left-sided CHD cases. Enrichment testing of gene content in all identified CNVs showed a significant association with angiogenesis. In this first family-based CNV study of left-sided CHD, we found that both co-segregating and de novo events associate with disease in a complex fashion at structural genomic level. Often viewed as an anatomically circumscript disease, a subset of left-sided CHD may in fact reflect more general genetic perturbations of angiogenesis and/or vascular biology.
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Khuong-Quang DA, Buczkowicz P, Rakopoulos P, Liu XY, Fontebasso AM, Bouffet E, Bartels U, Albrecht S, Schwartzentruber J, Letourneau L, Bourgey M, Bourque G, Montpetit A, Bourret G, Lepage P, Fleming A, Lichter P, Kool M, von Deimling A, Sturm D, Korshunov A, Faury D, Jones DT, Majewski J, Pfister SM, Jabado N, Hawkins C. K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol 2012; 124:439-47. [PMID: 22661320 PMCID: PMC3422615 DOI: 10.1007/s00401-012-0998-0] [Citation(s) in RCA: 686] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 05/18/2012] [Accepted: 05/19/2012] [Indexed: 11/28/2022]
Abstract
Pediatric glioblastomas (GBM) including diffuse intrinsic pontine gliomas (DIPG) are devastating brain tumors with no effective therapy. Here, we investigated clinical and biological impacts of histone H3.3 mutations. Forty-two DIPGs were tested for H3.3 mutations. Wild-type versus mutated (K27M-H3.3) subgroups were compared for HIST1H3B, IDH, ATRX and TP53 mutations, copy number alterations and clinical outcome. K27M-H3.3 occurred in 71 %, TP53 mutations in 77 % and ATRX mutations in 9 % of DIPGs. ATRX mutations were more frequent in older children (p < 0.0001). No G34V/R-H3.3, IDH1/2 or H3.1 mutations were identified. K27M-H3.3 DIPGs showed specific copy number changes, including all gains/amplifications of PDGFRA and MYC/PVT1 loci. Notably, all long-term survivors were H3.3 wild type and this group of patients had better overall survival. K27M-H3.3 mutation defines clinically and biologically distinct subgroups and is prevalent in DIPG, which will impact future therapeutic trial design. K27M- and G34V-H3.3 have location-based incidence (brainstem/cortex) and potentially play distinct roles in pediatric GBM pathogenesis. K27M-H3.3 is universally associated with short survival in DIPG, while patients wild-type for H3.3 show improved survival. Based on prognostic and therapeutic implications, our findings argue for H3.3-mutation testing at diagnosis, which should be rapidly integrated into the clinical decision-making algorithm, particularly in atypical DIPG.
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Yauk CL, Lucas Argueso J, Auerbach SS, Awadalla P, Davis SR, DeMarini DM, Douglas GR, Dubrova YE, Elespuru RK, Glover TW, Hales BF, Hurles ME, Klein CB, Lupski JR, Manchester DK, Marchetti F, Montpetit A, Mulvihill JJ, Robaire B, Robbins WA, Rouleau GA, Shaughnessy DT, Somers CM, Taylor JG, Trasler J, Waters MD, Wilson TE, Witt KL, Bishop JB. Harnessing genomics to identify environmental determinants of heritable disease. Mutat Res 2012; 752:6-9. [PMID: 22935230 DOI: 10.1016/j.mrrev.2012.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/17/2012] [Accepted: 08/19/2012] [Indexed: 12/27/2022]
Abstract
Next-generation sequencing technologies can now be used to directly measure heritable de novo DNA sequence mutations in humans. However, these techniques have not been used to examine environmental factors that induce such mutations and their associated diseases. To address this issue, a working group on environmentally induced germline mutation analysis (ENIGMA) met in October 2011 to propose the necessary foundational studies, which include sequencing of parent-offspring trios from highly exposed human populations, and controlled dose-response experiments in animals. These studies will establish background levels of variability in germline mutation rates and identify environmental agents that influence these rates and heritable disease. Guidance for the types of exposures to examine come from rodent studies that have identified agents such as cancer chemotherapeutic drugs, ionizing radiation, cigarette smoke, and air pollution as germ-cell mutagens. Research is urgently needed to establish the health consequences of parental exposures on subsequent generations.
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Dyment DA, Cader MZ, Chao MJ, Lincoln MR, Morrison KM, Disanto G, Morahan JM, De Luca GC, Sadovnick AD, Lepage P, Montpetit A, Ebers GC, Ramagopalan SV. Exome sequencing identifies a novel multiple sclerosis susceptibility variant in the TYK2 gene. Neurology 2012; 79:406-11. [PMID: 22744673 DOI: 10.1212/wnl.0b013e3182616fc4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To identify rare variants contributing to multiple sclerosis (MS) susceptibility in a family we have previously reported with up to 15 individuals affected across 4 generations. METHODS We performed exome sequencing in a subset of affected individuals to identify novel variants contributing to MS risk within this unique family. The candidate variant was genotyped in a validation cohort of 2,104 MS trio families. RESULTS Four family members with MS were sequenced and 21,583 variants were found to be shared among these individuals. Refining the variants to those with 1) a predicted loss of function and 2) present within regions of modest haplotype sharing identified 1 novel mutation (rs55762744) in the tyrosine kinase 2 (TYK2) gene. A different polymorphism within this gene has been shown to be protective in genome-wide association studies. In contrast, the TYK2 variant identified here is a novel, missense mutation and was found to be present in 10/14 (72%) cases and 28/60 (47%) of the unaffected family members. Genotyping additional 2,104 trio families showed the variant to be transmitted preferentially from heterozygous parents (transmitted 16: not transmitted 5; χ(2) = 5.76, p = 0.016). CONCLUSIONS Rs55762744 is a rare variant of modest effect on MS risk affecting a subset of patients (0.8%). Within this pedigree, rs55762744 is common and appears to be a modifier of modest risk effect. Exome sequencing is a quick and cost-effective method and we show here the utility of sequencing a few cases from a single, unique family to identify a novel variant. The sequencing of additional family members or other families may help identify other variants important in MS.
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Shih CS, Ekoma S, Ho C, Pradhan K, Hwang E, Jakacki R, Fisher M, Kilburn L, Horn M, Vezina G, Rood B, Packer R, Mittal R, Omar S, Khalifa N, Bedir R, Avery R, Hwang E, Acosta M, Hutcheson K, Santos D, Zand D, Kilburn L, Rosenbaum K, Rood B, Packer R, Kalin-Hajdu E, Ospina L, Carret AS, Marzouki M, Decarie JC, Freeman E, Hershon L, Warmuth-Metz M, Zurakowski D, Bison B, Falkenstein F, Gnekow A, Ehrstedt C, Laurencikas E, Bjorklund AC, Stromberg B, Hedborg F, Pfeifer S, Bertin D, Packer RJ, Vallero S, Basso ME, Romano E, Peretta P, Morra I, D'Alonzo G, Fagioli F, Toledano H, Laviv Y, Dratviman-Storobinsky O, Michowiz S, Yaniv I, Cohen IJ, Goldenberg-Cohen N, Muller K, Gnekow A, Warmuth-Metz M, Pietsch T, Zwiener I, Falkenstein F, Meyer FM, Micke O, Hoffmann W, Kortmann RD, Shofty B, Ben-Sira L, Roth J, Constantini S, Shofty B, Weizmann L, Joskowicz L, Kesler A, Ben-Bashat D, Yalon M, Dvir R, Freedman S, Roth J, Ben-Sira L, Constantini S, Bandopadhayay P, Dagi L, Robison N, Goumnerova L, Ullrich N, Opocher E, De Salvo GL, De Paoli A, Simmons I, Sehested A, Walker DA, Picton SV, Gnekow A, Grill J, Driever PH, Azizi AA, Viscardi E, Perilongo G, Cappellano AM, Bouffet E, Silva F, Paiva P, Cavalheiro S, Seixas MT, Silva NS, Antony R, Fraser K, Lin J, Falkenstein F, Kwiecien R, Mirow C, Thieme B, von Hornstein S, Pietsch T, Faldum A, Warmuth-Metz M, Kortmann RD, Gnekow AK, Shofty B, Bokshtein F, Kesler A, Ben-Sira L, Freedman S, Constantini S, Panandiker AP, Klimo P, Thompson C, Armstrong G, Kun L, Boop F, Sanford A, Orge F, Laschinger K, Gold D, Bangert B, Stearns D, Cappellano AM, Senerchia A, Paiva P, Cavalheiro S, Silva F, Silva NS, Gnekow AK, Falkenstein F, Walker D, Perilongo G, Picton S, Grill J, Kortmann RD, Stokland T, van Meeteren AS, Slavc I, Faldum A, de Salvo GL, Fernandez KS, Antony R, Lulla RR, Flores M, Benavides VC, Mitchell C, AlKofide A, Hassonah M, Khafagh Y, Ayas MA, AlFawaz I, Anas M, Barria M, Siddiqui K, Al-Shail E, Fisher MJ, Ullrich NJ, Ferner RE, Gutmann DH, Listernick R, Packer RJ, Tabori U, Hoffman RO, Ardern-Holmes SL, Hummel TR, Hargrave DR, Charrow J, Loguidice M, Balcer LJ, Liu GT, Fisher MJ, Listernick R, Gutmann DH, Ferner RE, Packer RJ, Ullrich NJ, Tabori U, Hoffman RO, Ardern-Holmes SL, Hummel TR, Hargrave DR, Loguidice M, Balcer LJ, Liu GT, Jeeva I, Nelson O, Guy D, Damani A, Gogi D, Picton S, Simmons I, Jeeva I, Picton S, Guy D, Nelson O, Dewsbery S, Gogi D, Simmons I, Sievert AJ, Lang SS, Boucher K, Slaunwhite E, Brewington D, Madsen P, Storm PB, Resnick AC, Hemenway M, Madden J, Macy M, Foreman N, Rush S, Mascelli S, Raso A, Barla A, Nozza P, Biassoni R, Pignatelli S, Cama A, Verri A, Capra V, Garre M, Bergthold G, Piette C, Raquin MA, Dufour C, Varlet P, Dhermain F, Puget S, Sainte-Rose C, Abely M, Canale S, Grill J, Terashima K, Chow K, Jones J, Ahern C, Jo E, Ellezam B, Paulino A, Okcu MF, Su J, Adesina A, Mahajan A, Dauser R, Whitehead W, Lau C, Chintagumpala M, Kebudi R, Tuncer S, Cakir FB, Gorgun O, Agaoglu FY, Ayan I, Darendeliler E, Wolf D, Cohen K, Jeyapalan JN, Morley ICF, Hill AA, Tatevossian RG, Qaddoumi I, Ellison DW, Sheer D, Donson A, Barton V, Birks D, Kleinschmidt-DeMasters BK, Hemenway M, Handler M, Foreman N, Rush S, Tatevossian R, Qaddoumi I, Tang B, Dalton J, Shurtleff S, Punchihewa C, Orisme W, Neale G, Gajjar A, Baker S, Sheer D, Ellison D, Gilheeney S, Jamzadeh A, Winchester M, Yataghene K, De Braganca K, Khakoo Y, Lyden D, Dunkel I, Terasaki M, Eto T, Morioka M, Ho CY, Bar E, Giannini C, Karajannis MA, Zagzag D, Eberhart CG, Rodriguez FJ, Lee Y, Bartels U, Tabori U, Huang A, Bouffet E, Zaky W, Bluml S, Grimm J, Wong K, McComb G, Gilles F, Finlay J, Dhall G, Chen HH, Chen YW, Chang FC, Lin SC, Chang KP, Ho DM, Wong TT, Lee CC, Azizi AA, Fox R, Grill J, Mirow C, Gnekow A, Walker D, Perilongo G, Opocher E, Wheatley K, van Meeteren AYS, Phuakpet K, Tabori U, Bartels U, Huang A, Kulkarni A, Laperriere N, Bouffet E, Epari S, Nair V, Gupta T, Patil P, Moiyadi A, Shetty P, Kane S, Jalali R, Dorris K, Nadi M, Sutton M, Wang L, Stogner K, Li D, Hurwitz B, Stevenson C, Miles L, Kim MO, Fuller C, Hawkins C, Bouffet E, Jones B, Drake J, Fouladi M, Fontebasso AM, Shirinian M, Jones DTW, Quang DAK, Jacob K, Cin H, Witt H, Gerges N, Montpetit A, Brunet S, Lepage P, Klekner A, Lambert S, Kwan T, Hawkins C, Tabori U, Collins VP, Albrecht S, Pfister SM, Jabado N, Arrington D, Manley P, Kieran M, Chi S, Robison N, Chordas C, Ullrich N. LOW GRADE GLIOMAS. Neuro Oncol 2012; 14:i69-i81. [PMCID: PMC3483338 DOI: 10.1093/neuonc/nos092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
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Lanktree M, Guo Y, Murtaza M, Glessner J, Bailey S, Onland-Moret N, Lettre G, Ongen H, Rajagopalan R, Johnson T, Shen H, Nelson C, Klopp N, Baumert J, Padmanabhan S, Pankratz N, Pankow J, Shah S, Taylor K, Barnard J, Peters B, Maloney C, Lobmeyer M, Stanton A, Zafarmand M, Romaine S, Mehta A, van Iperen E, Gong Y, Price T, Smith E, Kim C, Li Y, Asselbergs F, Atwood L, Bailey K, Bhatt D, Bauer F, Behr E, Bhangale T, Boer J, Boehm B, Bradfield J, Brown M, Braund P, Burton P, Carty C, Chandrupatla H, Chen W, Connell J, Dalgeorgou C, de Boer A, Drenos F, Elbers C, Fang J, Fox C, Frackelton E, Fuchs B, Furlong C, Gibson Q, Gieger C, Goel A, Grobbee D, Hastie C, Howard P, Huang GH, Johnson W, Li Q, Kleber M, Klein B, Klein R, Kooperberg C, Ky B, LaCroix A, Lanken P, Lathrop M, Li M, Marshall V, Melander O, Mentch F, Meyer N, Monda K, Montpetit A, Murugesan G, Nakayama K, Nondahl D, Onipinla A, Rafelt S, Newhouse S, Otieno F, Patel S, Putt M, Rodriguez S, Safa R, Sawyer D, Schreiner P, Simpson C, Sivapalaratnam S, Srinivasan S, Suver C, Swergold G, Sweitzer N, Thomas K, Thorand B, Timpson N, Tischfield S, Tobin M, Tomaszewski M, Verschuren W, Wallace C, Winkelmann B, Zhang H, Zheng D, Zhang L, Zmuda J, Clarke R, Balmforth A, Danesh J, Day I, Schork N, de Bakker P, Delles C, Duggan D, Hingorani A, Hirschhorn J, Hofker M, Humphries S, Kivimaki M, Lawlor D, Kottke-Marchant K, Mega J, Mitchell B, Morrow D, Palmen J, Redline S, Shields D, Shuldiner A, Sleiman P, Smith G, Farrall M, Jamshidi Y, Christiani D, Casas J, Hall A, Doevendans P, Christie J, Berenson G, Murray S, Illig T, Dorn G, Cappola T, Boerwinkle E, Sever P, Rader D, Reilly M, Caulfield M, Talmud P, Topol E, Engert J, Wang K, Dominiczak A, Hamsten A, Curtis S, Silverstein R, Lange L, Sabatine M, Trip M, Saleheen D, Peden J, Cruickshanks K, März W, O'Connell J, Klungel O, Wijmenga C, Maitland-van der Zee A, Schadt E, Johnson J, Jarvik G, Papanicolaou G, Grant S, Munroe P, North K, Samani N, Koenig W, Gaunt T, Anand S, van der Schouw Y, Soranzo N, FitzGerald G, Reiner A, Hegele R, Hakonarson H, Keating B. Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Am J Hum Genet 2012. [DOI: 10.1016/j.ajhg.2012.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Spinella JF, Saillour V, Richer C, Ouimet M, Cassart P, Healy J, Bareke E, Larivière M, St-Onge P, Busche S, Ge B, Montpetit A, Pastinen T, Sinnett D. Abstract 4335: The genomic landscape of childhood pre-B acute lymphoblastic leukemia. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Precursor B-cell acute lymphoblastic leukemia (pre-B ALL) is the most frequent pediatric cancer. Increased understanding of the pathobiology of B-cell ALL has led to risk-targeted treatment regimens and increased survival rates. However, the underlying causes of this pediatric cancer are still unclear. We are using next-generation sequencing technology to better understand the genomic landscape of pre-B ALL and to build a catalogue of variations involved in pediatric ALL onset and/or progression. Using a unique “quartet” design that involves matched tumor (at diagnosis) and normal (remission) samples, as well as DNA from both parents, we will be able to identify somatic mutations driving the leukemic process. Here, we report the deep-sequencing of the whole exomes, and the partial miRNomes, of over 60 childhood B-cell ALL quartets. Using ABI SOLiD technology, we captured over 4.0 Gb of sequence on average per sample with a mean coverage of 40X. Genome-wide genotyping (Illumina's Omni 2.5 array) was also for quality control and structural variant identification. For each individual, approximately 97% of the targeted region was covered α1X and 80% of the targeted bases passed our thresholds for variant calling (≥ 5X coverage, MQV ≤ 20). According to these criteria, about 25,000 SNPs were found per individual. Using this quartet design we were able to incorporate parental sequence information to reduce sequencing errors and facilitate the identification of true variants within a given family, and of leukemia-specific variants within the ALL cohort. We investigated the somatic mutation profiles of the ALL genomes and identified both recurrent and private leukemia-specific mutations, and highlighted genes/pathways with an increased burden of somatic loss of function variants. Our goal now is to validate potential driver mutations that could play a direct role in leukemogenesis through functional assessment. Ultimately, this work will provide invaluable insights to understand the genetic mechanisms underlying pediatric ALL which could lead to the development of powerful clinical tools to improve detection, diagnosis and treatment of this childhood cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4335. doi:1538-7445.AM2012-4335
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Healy J, Saillour V, Spinella JF, Vidal R, Bareke E, Richer C, Larivière M, Busche S, Ge B, Montpetit A, Pastinen T, Sinnett D. Abstract 2484: Whole-exome sequencing of a rare case of familial childhood acute lymphoblastic leukemia. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-2484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children, accounting for approximately 25% of all pediatric cancer cases. However, familial childhood ALL is extremely rare. Few families with multiple non-twinned siblings diagnosed with childhood ALL have been reported, and to date no highly penetrant leukemia susceptibility gene(s) has been identified to explain this uncommon occurrence. We postulated that pure (nonsyndromic) familial childhood ALL could result from the accumulation of disadvantaging rare DNA variants in predisposing genes or biological pathways. To address this hypothesis, we used next-generation sequencing technologies to capture and re-sequence the whole-exomes of a family comprising the mother, father and two male non-twinned affected siblings (sibling A and sibling B). Both brothers were diagnosed with the identical ALL subtype, pre-B hyperdiploid childhood ALL, three years apart. The similar clinical and molecular characteristics of the siblings suggest shared etiologic factors. Using the Agilent SureSelect All Human Exon 38 Mb Kit and the SOLiD 3 Plus system, we captured and sequenced a total of 17.5 Gb of sequence for the entire family, with a mean coverage of 47X. For each individual, approximately 96% or 36.4 Mb of the targeted bases were covered α1X and 70% of the targeted bases or 26.4 Mb passed our thresholds for variant calling. We identified 52,038 positions at which the called allele(s) differed from the reference genome in at least one of the four family members. In total, we identified 19,096 germline variants in sibling A and 28,061 in sibling B, of which 2,355 (12.3%) and 2,125 (7.6%), respectively, were previously undiscovered in dbSNP. We investigated non-synonymous homozygous variant and compound heterozygous positions shared between the siblings, as well as genes/pathways with increased burden of rare non-synonymous variants. Based on several criteria (PolyPhen annotation, known allele frequency, etc.), we identified variants that are strong functional candidates to explain this case of pure familial childhood ALL. In parallel, high-density genotyping was also performed (Illumina Omni 2.5M) for quality control and structural variant detection, allowing the identification of putatively shared copy number variants that may also be involved in leukemogenesis. Though independent validation and functional assessment is required, this is the first study to identify genetic factors involved in pure familial childhood ALL.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2484. doi:1538-7445.AM2012-2484
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Rousseau J, Chapdelaine P, Boisvert S, Almeida LP, Corbeil J, Montpetit A, Tremblay JP. Endonucleases: tools to correct the dystrophin gene. J Gene Med 2012; 13:522-37. [PMID: 21954090 DOI: 10.1002/jgm.1611] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Various endonucleases can be engineered to induce double-strand breaks (DSBs) in chosen DNA sequences. These DSBs are spontaneously repaired by nonhomologous-end-joining, resulting in micro-insertions or micro-deletions (INDELs). We detected, characterized and quantified the frequency of INDELs produced by one meganuclease (MGN) targeting the RAG1 gene, six MGNs targeting three introns of the human dystrophin gene and one pair of zinc finger nucleases (ZFNs) targeting exon 50 of the human dystrophin gene. The experiments were performed in human cells (i.e. 293 T cells, myoblasts and myotubes). METHODS To analyse the INDELs produced by the endonucleases the targeted region was polymerase chain reaction amplified and the amplicons were digested with the Surveyor enzyme, cloned in bacteria or deep sequenced. RESULTS Endonucleases targeting the dystrophin gene produced INDELs of different sizes but there were clear peaks in the size distributions. The positions of these peaks were similar for MGNs but not for ZFNs in 293 T cells and in myoblasts. The size of the INDELs produced by these endonucleases in the dystrophin gene would have permitted a change in the reading frame. In a subsequent experiment, we observed that the frequency of INDELs was increased by re-exposition of the cells to the same endonuclease. CONCLUSIONS Endonucleases are able to: (i) restore the normal reading of a gene with a frame shift mutation; (ii) delete a nonsense codon; and (iii) knockout a gene. Endonucleases could thus be used to treat Duchenne muscular dystrophy and other hereditary diseases that are the result of a nonsense codon or a frame shift mutation.
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Ramagopalan SV, Dyment DA, Cader MZ, Morrison KM, Disanto G, Morahan JM, Berlanga-Taylor AJ, Handel A, De Luca GC, Sadovnick AD, Lepage P, Montpetit A, Ebers GC. Rare variants in the CYP27B1 gene are associated with multiple sclerosis. Ann Neurol 2012; 70:881-6. [PMID: 22190362 DOI: 10.1002/ana.22678] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Multiple sclerosis (MS) is a complex neurological disease. Genetic linkage analysis and genotyping of candidate genes in families with 4 or more affected individuals more heavily loaded for susceptibility genes has not fully explained familial disease clustering. METHODS We performed whole exome sequencing to further understand the heightened prevalence of MS in these families. RESULTS Forty-three individuals with MS (1 from each family) were sequenced to find rare variants in candidate MS susceptibility genes. On average, >58,000 variants were identified in each individual. A rare variant in the CYP27B1 gene causing complete loss of gene function was identified in 1 individual. Homozygosity for this mutation results in vitamin D-dependent rickets I (VDDR1), whereas heterozygosity results in lower calcitriol levels. This variant showed significant heterozygous association in 3,046 parent-affected child trios (p = 1 × 10(-5)). Further genotyping in >12,500 individuals showed that other rare loss of function CYP27B1 variants also conferred significant risk of MS, Peto odds ratio = 4.7 (95% confidence interval, 2.3-9.4; p = 5 × 10(-7)). Four known VDDR1 mutations were identified, all overtransmitted. Heterozygous parents transmitted these alleles to MS offspring 35 of 35× (p = 3 × 10(-9)). INTERPRETATION A causative role for CYP27B1 in MS is supported; the mutations identified are known to alter function having been shown in vivo to result in rickets when 2 copies are present. CYP27B1 encodes the vitamin D-activating 1-alpha hydroxylase enzyme, and thus a role for vitamin D in MS pathogenesis is strongly implicated.
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Schwartzentruber J, Korshunov A, Liu XY, Jones DTW, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DAK, Tönjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jäger N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Frühwald MC, Roggendorf W, Kramm C, Dürken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 2012. [PMID: 22286061 DOI: 10.1038/nature11026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glioblastoma multiforme (GBM) is a lethal brain tumour in adults and children. However, DNA copy number and gene expression signatures indicate differences between adult and paediatric cases. To explore the genetic events underlying this distinction, we sequenced the exomes of 48 paediatric GBM samples. Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway were identified in 44% of tumours (21/48). Recurrent mutations in H3F3A, which encodes the replication-independent histone 3 variant H3.3, were observed in 31% of tumours, and led to amino acid substitutions at two critical positions within the histone tail (K27M, G34R/G34V) involved in key regulatory post-translational modifications. Mutations in ATRX (α-thalassaemia/mental retardation syndrome X-linked) and DAXX (death-domain associated protein), encoding two subunits of a chromatin remodelling complex required for H3.3 incorporation at pericentric heterochromatin and telomeres, were identified in 31% of samples overall, and in 100% of tumours harbouring a G34R or G34V H3.3 mutation. Somatic TP53 mutations were identified in 54% of all cases, and in 86% of samples with H3F3A and/or ATRX mutations. Screening of a large cohort of gliomas of various grades and histologies (n = 784) showed H3F3A mutations to be specific to GBM and highly prevalent in children and young adults. Furthermore, the presence of H3F3A/ATRX-DAXX/TP53 mutations was strongly associated with alternative lengthening of telomeres and specific gene expression profiles. This is, to our knowledge, the first report to highlight recurrent mutations in a regulatory histone in humans, and our data suggest that defects of the chromatin architecture underlie paediatric and young adult GBM pathogenesis.
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Prithviraj GK, Sommers SR, Jump RL, Halmos B, Chambless LB, Parker SL, Hassam-Malani L, McGirt MJ, Thompson RC, Chambless LB, Parker SL, Hassam-Malani L, McGirt MJ, Thompson RC, Hunter K, Chamberlain MC, Le EM, Lee ELT, Chamberlain MC, Sadighi ZS, Pearlman ML, Slopis JM, Vats TS, Khatua S, DeVito NC, Yu M, Chen R, Pan E, Cloughesy T, Raizer J, Drappatz J, Gerena-Lewis M, Rogerio J, Yacoub S, Desjardin A, Groves MD, DeGroot J, Loghin M, Conrad CA, Hess K, Ni J, Ictech S, Hunter K, Yung WA, Porter AB, Dueck AC, Karlin NJ, Chamberlain MC, Olson J, Silber J, Reiner AS, Panageas KS, Iwamoto FM, Cloughesy TF, Aldape KD, Rivera AL, Eichler AF, Louis DN, Paleologos NA, Fisher BJ, Ashby LS, Cairncross JG, Roldan GB, Wen PY, Ligon KL, Shiff D, Robins HI, Rocque BG, Chamberlain MC, Mason WP, Weaver SA, Green RM, Kamar FG, Abrey LE, DeAngelis LM, Jhanwar SC, Rosenblum MK, Lassman AB, Cachia D, Alderson L, Moser R, Smith T, Yunus S, Saito K, Mukasa A, Narita Y, Tabei Y, Shinoura N, Shibui S, Saito N, Flechl B, Ackerl M, Sax C, Dieckmann K, Crevenna R, Widhalm G, Preusser M, Marosi C, Marosi C, Ay C, Preusser M, Dunkler D, Widhalm G, Pabinger I, Dieckmann K, Zielinski C, Belongia M, Jogal S, Schlingensiepen KH, Bogdahn U, Stockhammer G, Mahapatra AK, Venkataramana NK, Oliushine V, Parfenov V, Poverennova I, Hau P, Jachimczak P, Heinrichs H, Mammoser AG, Shonka NA, de Groot JF, Shibahara I, Sonoda Y, Kumabe T, Saito R, Kanamori M, Yamashita Y, Watanabe M, Ishioka C, Tominaga T, Silvani A, Gaviani P, Lamperti E, Botturi A, DiMeco F, Broggi G, Fariselli L, Solero CL, Salmaggi A, Green RM, Woyshner EA, Cloughesy TF, Shu F, Oh YS, Iganej S, Singh G, Vemuri SL, Theeler BJ, Ellezam B, Gilbert MR, Aoki T, Kobayashi H, Takano S, Nishikawa R, Shinoura N, Nagane M, Narita Y, Muragaki Y, Sugiyama K, Kuratsu J, Matsutani M, Sadighi ZS, Khatua S, Langford LA, Puduvalli VK, Shen D, Chen ZP, Zhang JP, Chen ZP, Bedekar D, Rand S, Connelly J, Malkin M, Paulson E, Mueller W, Schmainda K, Gallego O, Benavides M, Segura PP, Balana C, Gil M, Berrocal A, Reynes G, Garcia JL, Murata P, Bague S, Quintana MJ, Vasishta VG, Nagane M, Kobayashi K, Tanaka M, Tsuchiya K, Shiokawa Y, Bavle AA, Ayyanar K, Puduvalli VK, Prado MP, Hess KR, Hunter K, Ictech S, Groves MD, Gilbert MR, Liu V, Conrad CA, de Groot J, Loghin ME, Colman H, Levin VA, Alfred Yung WK, Hackney JR, Palmer CA, Markert JM, Cure J, Riley KO, Fathallah-Shaykh H, Nabors LB, Saria MG, Corle C, Hu J, Rudnick J, Phuphanich S, Mrugala MM, Lee LK, Fu BD, Bota DA, Kim RY, Brown T, Feely H, Hu A, Drappatz J, Wen PY, Lee JW, Carter B, Kesari S, Fu BD, Kong XT, Bota DA, Fu BD, Bota DA, Sparagana S, Belousova E, Jozwiak S, Korf B, Frost M, Kuperman R, Kohrman M, Witt O, Wu J, Flamini R, Jansen A, Curtalolo P, Thiele E, Whittemore V, De Vries P, Ford J, Shah G, Cauwel H, Edrich P, Sahmoud T, Franz D, Khasraw M, Brown C, Ashley DM, Rosenthal MA, Jiang X, Mou YG, Chen ZP, Oh M, kim E, Chang J, Juratli TA, Kirsch M, Schackert G, Krex D, Gilbert MR, Wang M, Aldape KD, Stupp R, Hegi M, Jaeckle KA, Armstrong TS, Wefel JS, Won M, Blumenthal DT, Mahajan A, Schultz CJ, Erridge SC, Brown PD, Chakravarti A, Curran WJ, Mehta MP, Hofland KF, Hansen S, Sorensen M, Schultz H, Muhic A, Engelholm S, Ask A, Kristiansen C, Thomsen C, Poulsen HS, Lassen UN, Zalatimo O, Weston C, Zoccoli C, Glantz M, Rahmanuddin S, Shiroishi MS, Cen SY, Jones J, Chen T, Pagnini P, Go J, Lerner A, Gomez J, Law M, Ram Z, Wong ET, Gutin PH, Bobola MS, Alnoor M, Silbergeld DL, Rostomily RC, Chamberlain MC, Silber JR, Martha N, Jacqueline S, Thaddaus G, Daniel P, Hans M, Armin M, Eugen T, Gunther S, Hutterer M, Tseng HM, Zoccoli CM, Glantz M, Zalatimo O, Patel A, Rizzo K, Sheehan JM, Sumrall AL, Vredenburgh JJ, Desjardins A, Reardon DA, Friiedman HS, Peters KB, Taylor LP, Stewart M, Blondin NA, Baehring JM, Foote T, Laack N, Call J, Hamilton MG, Walling S, Eliasziw M, Easaw J, Shirsat NV, Kundar R, Gokhale A, Goel A, Moiyadi AA, Wang J, Mutlu E, Oyan A, Yan T, Tsinkalovsky O, Jacobsen HK, Talasila KM, Sleire L, Pettersen K, Miletic H, Andersen S, Mitra S, Weissman I, Li X, Kalland KH, Enger PO, Sepulveda J, Belda C, Balana C, Segura PP, Reynes G, Gil M, Gallego O, Berrocal A, Blumenthal DT, Sitt R, Phishniak L, Bokstein F, Philippe M, Carole C, Andre MDP, Marylin B, Olivier C, L'Houcine O, Dominique FB, Philippe M, Isabelle NM, Olivier C, Frederic F, Stephane F, Henry D, Marylin B, L'Houcine O, Dominique FB, Errico MA, Kunschner LJ, Errico MA, Kunschner LJ, Soffietti R, Trevisan E, Ruda R, Bertero L, Bosa C, Fabrini MG, Lolli I, Jalali R, Julka PK, Anand AK, Bhavsar D, Singhal N, Naik R, John S, Mathew BS, Thaipisuttikul I, Graber J, DeAngelis LM, Shirinian M, Fontebasso AM, Jacob K, Gerges N, Montpetit A, Nantel A, Albrecht S, Jabado N, Mammoser AG, Shah K, Conrad CA, Di K, Linskey M, Bota DA, Thon N, Eigenbrod S, Kreth S, Lutz J, Tonn JC, Kretzschmar H, Peraud A, Kreth FW, Muggeri AD, Alderuccio JP, Diez BD, Jiang P, Chao Y, Gallagher M, Kim R, Pastorino S, Fogal V, Kesari S, Rudnick JD, Bresee C, Rogatko A, Sakowsky S, Franco M, Hu J, Lim S, Lopez A, Yu L, Ryback K, Tsang V, Lill M, Steinberg A, Sheth R, Grimm S, Helenowski I, Rademaker A, Raizer J, Nunes FP, Merker V, Jennings D, Caruso P, Muzikansky A, Stemmer-Rachamimov A, Plotkin S, Spalding AC, Vitaz TW, Sun DA, Parsons S, Welch MR, Omuro A, DeAngelis LM, Omuro A, Beal K, Correa D, Chan T, DeAngelis L, Gavrilovic I, Nolan C, Hormigo A, Lassman AB, Kaley T, Mellinghoff I, Grommes C, Panageas K, Reiner A, Barradas R, Abrey L, Gutin P, Lee SY, Slagle-Webb B, Glantz MJ, Sheehan JM, Connor JR, Schlimper CA, Schlag H, Stoffels G, Weber F, Krueger DA, Care MM, Holland K, Agricola K, Tudor C, Byars A, Sahmoud T, Franz DN, Raizer J, Rice L, Rademaker A, Chandler J, Levy R, Muro K, Grimm S, Nayak L, Iwamoto FM, Rudnick JD, Norden AD, Omuro A, Kaley TJ, Thomas AA, Fadul CE, Meyer LP, Lallana EC, Colman H, Gilbert M, Alfred Yung WK, Aldape K, De Groot J, Conrad C, Levin V, Groves M, Loghin M, Chris P, Puduvalli V, Nagpal S, Feroze A, Recht L, Rangarajan HG, Kieran MW, Scott RM, Lew SM, Firat SY, Segura AD, Jogal SA, Kumthekar PU, Grimm SA, Avram M, Patel J, Kaklamani V, McCarthy K, Cianfrocca M, Gradishar W, Mulcahy M, Von Roenn J, Helenowski I, Rademaker A, Raizer J, Galanis E, Anderson SK, Lafky JM, Kaufmann TJ, Uhm JH, Giannini C, Kumar SK, Northfelt DW, Flynn PJ, Jaeckle KA, Buckner JC, Omar AI, Panageas KS, Iwamoto FM, Cloughesy TF, Aldape KD, Rivera AL, Eichler AF, Louis DN, Paleologos NA, Fisher BJ, Ashby LS, Cairncross JG, Roldan GB, Wen PY, Ligon KL, Schiff D, Robins HI, Rocque BG, Chamberlain MC, Mason WP, Weaver SA, Green RM, Kamar FG, Abrey LE, DeAngelis LM, Jhanwar SC, Rosenblum MK, Lassman AB, Delios A, Jakubowski A, DeAngelis L, Grommes C, Lassman AB, Theeler BJ, Melguizo-Gavilanes I, Shonka NA, Qiao W, Wang X, Mahajan A, Puduvalli V, Hashemi-Sadraei N, Bawa H, Rahmathulla G, Patel M, Elson P, Stevens G, Peereboom D, Vogelbaum M, Weil R, Barnett G, Ahluwalia MS, Alvord EC, Rockne RC, Rockhill JK, Mrugala MM, Rostomily R, Lai A, Cloughesy T, Wardlaw J, Spence AM, Swanson KR, Zadeh G, Alahmadi H, Wilson J, Gentili F, Lassman AB, Wang M, Gilbert MR, Aldape KD, Beumer JJ, Wright J, Takebe N, Puduvalli VK, Hormigo A, Gaur R, Werner-Wasik M, Mehta MP, Gupta AJ, Campos-Gines A, Le K, Arango C, Richards M, Landeros M, Juan H, Chang JH, Kim JS, Cho JH, Seo CO, Baldock AL, Rockne R, Canoll P, Born D, Yagle K, Swanson KR, Alexandru D, Bota D, Linskey ME, Nabeel S, Raval SN, Raizer J, Grimm S, Rice L, Rosenow J, Levy R, Bredel M, Chandler J, New PZ, Plotkin SR, Supko JG, Curry WT, Chi AS, Gerstner ER, Stemmer-Rachamimov A, Batchelor TT, Ahluwalia MS, Hashemi N, Rahmathulla G, Patel M, Chao ST, Peereboom D, Weil RJ, Suh JH, Vogelbaum MA, Stevens GH, Barnett GH, Corwin D, Holdsworth C, Stewart R, Rockne R, Swanson K, Graber JJ, Kaley T, Rockne RC, Anderson AR, Swanson KR, Jeyapalan S, Goldman M, Boxerman J, Donahue J, Elinzano H, Evans D, O'Connor B, Puthawala MY, Oyelese A, Cielo D, Blitstein M, Dargush M, Santaniello A, Constantinou M, DiPetrillo T, Safran H, Plotkin SR, Halpin C, Merker V, Barker FG, Maher EA, Ganji S, DeBerardinis R, Hatanpaa K, Rakheja D, Yang XL, Mashimo T, Raisanen J, Madden C, Mickey B, Malloy C, Bachoo R, Choi C, Ranjan T, Yono N, Zalatimo O, Zoccoli C, Glantz M, Han SJ, Sun M, Berger MS, Aghi M, Gupta N, Parsa AT. MEDICAL AND NEURO-ONCOLOGY. Neuro Oncol 2011. [DOI: 10.1093/neuonc/nor152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N. What can exome sequencing do for you? J Med Genet 2011. [PMID: 21730106 DOI: 10.1136/jmedgenet‐2011‐100223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Recent advances in next-generation sequencing technologies have brought a paradigm shift in how medical researchers investigate both rare and common human disorders. The ability cost-effectively to generate genome-wide sequencing data with deep coverage in a short time frame is replacing approaches that focus on specific regions for gene discovery and clinical testing. While whole genome sequencing remains prohibitively expensive for most applications, exome sequencing--a technique which focuses on only the protein-coding portion of the genome--places many advantages of the emerging technologies into researchers' hands. Recent successes using this technology have uncovered genetic defects with a limited number of probands regardless of shared genetic heritage, and are changing our approach to Mendelian disorders where soon all causative variants, genes and their relation to phenotype will be uncovered. The expectation is that, in the very near future, this technology will enable us to identify all the variants in an individual's personal genome and, in particular, clinically relevant alleles. Beyond this, whole genome sequencing is also expected to bring a major shift in clinical practice in terms of diagnosis and understanding of diseases, ultimately enabling personalised medicine based on one's genome. This paper provides an overview of the current and future use of next generation sequencing as it relates to whole exome sequencing in human disease by focusing on the technical capabilities, limitations and ethical issues associated with this technology in the field of genetics and human disease.
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Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N. What can exome sequencing do for you? J Med Genet 2011; 48:580-9. [PMID: 21730106 DOI: 10.1136/jmedgenet-2011-100223] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Recent advances in next-generation sequencing technologies have brought a paradigm shift in how medical researchers investigate both rare and common human disorders. The ability cost-effectively to generate genome-wide sequencing data with deep coverage in a short time frame is replacing approaches that focus on specific regions for gene discovery and clinical testing. While whole genome sequencing remains prohibitively expensive for most applications, exome sequencing--a technique which focuses on only the protein-coding portion of the genome--places many advantages of the emerging technologies into researchers' hands. Recent successes using this technology have uncovered genetic defects with a limited number of probands regardless of shared genetic heritage, and are changing our approach to Mendelian disorders where soon all causative variants, genes and their relation to phenotype will be uncovered. The expectation is that, in the very near future, this technology will enable us to identify all the variants in an individual's personal genome and, in particular, clinically relevant alleles. Beyond this, whole genome sequencing is also expected to bring a major shift in clinical practice in terms of diagnosis and understanding of diseases, ultimately enabling personalised medicine based on one's genome. This paper provides an overview of the current and future use of next generation sequencing as it relates to whole exome sequencing in human disease by focusing on the technical capabilities, limitations and ethical issues associated with this technology in the field of genetics and human disease.
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Tucker T, Montpetit A, Chai D, Chan S, Chénier S, Coe BP, Delaney A, Eydoux P, Lam WL, Langlois S, Lemyre E, Marra M, Qian H, Rouleau GA, Vincent D, Michaud JL, Friedman JM. Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation. BMC Med Genomics 2011; 4:25. [PMID: 21439053 PMCID: PMC3076225 DOI: 10.1186/1755-8794-4-25] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 03/25/2011] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Clinical laboratories are adopting array genomic hybridization as a standard clinical test. A number of whole genome array genomic hybridization platforms are available, but little is known about their comparative performance in a clinical context. METHODS We studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500 K GeneChip SNP arrays, Agilent Human Genome 244 K oligonucleotide arrays and NimbleGen 385 K Whole-Genome oligonucleotide arrays. We also determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32 K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP arrays. RESULTS The Affymetrix 500 K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosomal CNVs in the 30 trios. 147 of these CNVs appeared to be de novo, but only 34 (22%) were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 most likely pathogenic and 2 possibly pathogenic CNVs for MR. All 9 of these putatively pathogenic CNVs were detected by the Affymetrix 500 K, Agilent, NimbleGen and the Illumina arrays, and 5 were found by the SMRT BAC array. Both putatively pathogenic CNVs identified in the 15 trios tested with the Affymetrix 6.0 were identified by this platform. CONCLUSIONS Our findings demonstrate that different results are obtained with different platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls on each of the platforms supports the need for validating clinically important findings with a different technology.
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Morcos L, Ge B, Koka V, Lam KCL, Pokholok DK, Gunderson KL, Montpetit A, Verlaan DJ, Pastinen T. Genome-wide assessment of imprinted expression in human cells. Genome Biol 2011; 12:R25. [PMID: 21418647 PMCID: PMC3129675 DOI: 10.1186/gb-2011-12-3-r25] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/21/2011] [Accepted: 03/21/2011] [Indexed: 01/19/2023] Open
Abstract
Background Parent-of-origin-dependent expression of alleles, imprinting, has been suggested to impact a substantial proportion of mammalian genes. Its discovery requires allele-specific detection of expressed transcripts, but in some cases detected allelic expression bias has been interpreted as imprinting without demonstrating compatible transmission patterns and excluding heritable variation. Therefore, we utilized a genome-wide tool exploiting high density genotyping arrays in parallel measurements of genotypes in RNA and DNA to determine allelic expression across the transcriptome in lymphoblastoid cell lines (LCLs) and skin fibroblasts derived from families. Results We were able to validate 43% of imprinted genes with previous demonstration of compatible transmission patterns in LCLs and fibroblasts. In contrast, we only validated 8% of genes suggested to be imprinted in the literature, but without clear evidence of parent-of-origin-determined expression. We also detected five novel imprinted genes and delineated regions of imprinted expression surrounding annotated imprinted genes. More subtle parent-of-origin-dependent expression, or partial imprinting, could be verified in four genes. Despite higher prevalence of monoallelic expression, immortalized LCLs showed consistent imprinting in fewer loci than primary cells. Random monoallelic expression has previously been observed in LCLs and we show that random monoallelic expression in LCLs can be partly explained by aberrant methylation in the genome. Conclusions Our results indicate that widespread parent-of-origin-dependent expression observed recently in rodents is unlikely to be captured by assessment of human cells derived from adult tissues where genome-wide assessment of both primary and immortalized cells yields few new imprinted loci.
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Witola WH, Mui E, Hargrave A, Liu S, Hypolite M, Montpetit A, Cavailles P, Bisanz C, Cesbron-Delauw MF, Fournié GJ, McLeod R. NALP1 influences susceptibility to human congenital toxoplasmosis, proinflammatory cytokine response, and fate of Toxoplasma gondii-infected monocytic cells. Infect Immun 2011; 79:756-66. [PMID: 21098108 PMCID: PMC3028851 DOI: 10.1128/iai.00898-10] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/20/2010] [Accepted: 11/11/2010] [Indexed: 11/20/2022] Open
Abstract
NALP1 is a member of the NOD-like receptor (NLR) family of proteins that form inflammasomes. Upon cellular infection or stress, inflammasomes are activated, triggering maturation of proinflammatory cytokines and downstream cellular signaling mediated through the MyD88 adaptor. Toxoplasma gondii is an obligate intracellular parasite that stimulates production of high levels of proinflammatory cytokines that are important in innate immunity. In this study, susceptibility alleles for human congenital toxoplasmosis were identified in the NALP1 gene. To investigate the role of the NALP1 inflammasome during infection with T. gondii, we genetically engineered a human monocytic cell line for NALP1 gene knockdown by RNA interference. NALP1 silencing attenuated progression of T. gondii infection, with accelerated host cell death and eventual cell disintegration. In line with this observation, upregulation of the proinflammatory cytokines interleukin-1β (IL-1β), IL-18, and IL-12 upon T. gondii infection was not observed in monocytic cells with NALP1 knockdown. These findings suggest that the NALP1 inflammasome is critical for mediating innate immune responses to T. gondii infection and pathogenesis. Although there have been recent advances in understanding the potent activity of inflammasomes in directing innate immune responses to disease, this is the first report, to our knowledge, on the crucial role of the NALP1 inflammasome in the pathogenesis of T. gondii infections in humans.
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Tremblay N, Yang SW, Hitz MP, Asselin G, Ginns J, Riopel K, Gendron R, Montpetit A, Duhig E, Dubé MP, Radford D, Andelfinger G. Familial ventricular aneurysms and septal defects map to chromosome 10p15. Eur Heart J 2010; 32:568-73. [DOI: 10.1093/eurheartj/ehq447] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Do R, Bailey SD, Paré G, Montpetit A, Desbiens K, Hudson TJ, Yusuf S, Bouchard C, Gaudet D, Pérusse L, Anand S, Vohl MC, Pastinen T, Engert JC. Fine Mapping of the Insulin-Induced Gene 2 Identifies a Variant Associated With LDL Cholesterol and Total Apolipoprotein B Levels. ACTA ACUST UNITED AC 2010; 3:454-61. [DOI: 10.1161/circgenetics.109.917039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background—
In a whole-genome scan, a single nucleotide polymorphism (SNP) (rs7566605) upstream of the insulin-induced gene 2 (
INSIG2
) was shown to influence body mass index and obesity in the Framingham Heart Study, with replication of these results in an additional 4 of 5 studies. However, other studies could not replicate the association. Because
INSIG2
plays an important role in cholesterol biosynthesis, we hypothesized that human
INSIG2
variants might play a role in the regulation of plasma lipid and lipoprotein levels.
Methods and Results—
We selected tagging SNPs spanning >100 kb of
INSIG2
locus and sequenced 18 434 base pairs to discover novel SNPs. Thirty-two SNPs were genotyped in 645 individuals from the Quebec Family Study. Two SNPs (rs10490626 and rs12464355) were associated with plasma low-density lipoprotein cholesterol (LDL-C) (
P
<0.0015) and total apolipoprotein B (apoB) levels (
P
<0.014), whereas no association was found between any SNP and body mass index. We replicated the finding of rs10490626 for both LDL-C and total apoB in additional study samples, including 758 individuals from Saguenay–Lac St. Jean, Quebec (
P
=0.040 for LDL-C,
P
=0.044 for apoB), 3247 Europeans (
P
=0.028 for LDL-C,
P
=0.030 for apoB), and 1695 South Asians (
P
=0.0036 for LDL-C,
P
=0.034 for apoB) from the INTERHEART study (for LDL-C, the combined 2-sided
P
=6.2×10
−5
and for total apoB,
P
=0.0011). Furthermore, we identified a variant in the human sorbin and SH
3
-domain–containing-1 gene that was associated with
INSIG2
mRNA levels, and this SNP was shown to act in combination with rs10490626 to affect LDL-C (
P
=0.022) in the Quebec Family Study and in INTERHEART South Asians (
P
=0.019) and Europeans (
P
=0.052).
Conclusion—
These results suggest that
INSIG2
genetic variants may have a more direct role in lipid and lipoprotein metabolism than in obesity.
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Bailey SD, Xie C, Do R, Montpetit A, Diaz R, Mohan V, Keavney B, Yusuf S, Gerstein HC, Engert JC, Anand S. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. Diabetes Care 2010; 33:2250-3. [PMID: 20628086 PMCID: PMC2945168 DOI: 10.2337/dc10-0452] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Thiazolidinediones are used to treat type 2 diabetes. Their use has been associated with peripheral edema and congestive heart failure-outcomes that may have a genetic etiology. RESEARCH DESIGN AND METHODS We genotyped 4,197 participants of the multiethnic DREAM (Diabetes REduction Assessment with ramipril and rosiglitazone Medication) trial with a 50k single nucleotide polymorphisms (SNP) array, which captures ∼2000 cardiovascular, inflammatory, and metabolic genes. We tested 32,088 SNPs for an association with edema among Europeans who received rosiglitazone (n = 965). RESULTS One SNP, rs6123045, in NFATC2 was significantly associated with edema (odds ratio 1.89 [95% CI 1.47-2.42]; P = 5.32 × 10(-7), corrected P = 0.017). Homozygous individuals had the highest edema rate (hazard ratio 2.89, P = 4.22 × 10(-4)) when compared with individuals homozygous for the protective allele, with heterozygous individuals having an intermediate risk. The interaction between the SNP and rosiglitazone for edema was significant (P = 7.68 × 10(-3)). Six SNPs in NFATC2 were significant in both Europeans and Latin Americans (P < 0.05). CONCLUSIONS Genetic variation at the NFATC2 locus contributes to edema among individuals who receive rosiglitazone.
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Manolescu DC, El-Kares R, Lakhal-Chaieb L, Montpetit A, Bhat PV, Goodyer P. Newborn serum retinoic acid level is associated with variants of genes in the retinol metabolism pathway. Pediatr Res 2010; 67:598-602. [PMID: 20308937 DOI: 10.1203/pdr.0b013e3181dcf18a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Retinoic acid (RA) is a critical regulator of gene expression during embryonic development. In rodents, moderate maternal vitamin A deficiency leads to subtle morphogenetic defects and inactivation of RA pathway genes causes major disturbances of embryogenesis. In this study, we quantified RA in umbilical cord blood of 145 healthy full-term Caucasian infants from Montreal. Sixty seven percent of values were <10 nmol/L (84 were <0.07 nmol/L) and 33% had moderate or high levels. Variation in RA could not be explained by parallel variation in its precursor, retinol (ROL). However, we found that the (A) allele of the rs12591551 single nucleotide polymorphism (SNP) in the ALDH1A2 gene (ALDH1A2rs12591551(A)), occurring in 19% of newborns, was associated with 2.5-fold higher serum RA levels. ALDH1A2 encodes retinaldehyde dehydrogenase (RALDH) 2, which synthesizes RA in fetal tissues. We also found that homozygosity for the (A) allele of the rs12724719 SNP in the CRABP2 gene (CRABP2rs12724719(A/A)) was associated with 4.4-fold increase in umbilical cord serum RA. CRABP2 facilitates RA binding to its cognate receptor complex and transfer to the nucleus. We hypothesize that individual variation in RA pathway genes may account for subtle variations in RA-dependent human embryogenesis.
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El Kares R, Manolescu DC, Lakhal-Chaieb L, Montpetit A, Zhang Z, Bhat PV, Goodyer P. A human ALDH1A2 gene variant is associated with increased newborn kidney size and serum retinoic acid. Kidney Int 2010; 78:96-102. [PMID: 20375987 DOI: 10.1038/ki.2010.101] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nephron number varies widely between 0.3 and 1.3 million per kidney in humans. During fetal life, the rate of nephrogenesis is influenced by local retinoic acid (RA) level such that even moderate maternal vitamin A deficiency limits the final nephron number in rodents. Inactivation of genes in the RA pathway causes renal agenesis in mice; however, the impact of retinoids on human kidney development is unknown. To resolve this, we tested for associations between variants of genes involved in RA metabolism (ALDH1A2, CYP26A1, and CYP26B1) and kidney size among normal newborns. Homozygosity for a common (1 in 5) variant, rs7169289(G), within an Sp1 transcription factor motif of the ALDH1A2 gene, showed a significant 22% increase in newborn kidney volume when adjusted for body surface area. Infants bearing this allele had higher umbilical cord blood RA levels compared to those with homozygous wild-type ALDH1A2 rs7169289(A) alleles. Furthermore, the effect of the rs7169289(G) variant was evident in subgroups with or without a previously reported hypomorphic RET 1476(A) proto-oncogene allele that is critical in determining final nephron number. As maternal vitamin A deficiency is widespread in developing countries and may compromise availability of retinol for fetal RA synthesis, our study suggests that the ALDH1A2 rs7169289(G) variant might be protective for such individuals.
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Tan TG, Mui E, Cong H, Witola WH, Montpetit A, Muench SP, Sidney J, Alexander J, Sette A, Grigg ME, Maewal A, McLeod R. Identification of T. gondii epitopes, adjuvants, and host genetic factors that influence protection of mice and humans. Vaccine 2010; 28:3977-89. [PMID: 20347630 DOI: 10.1016/j.vaccine.2010.03.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 03/09/2010] [Accepted: 03/15/2010] [Indexed: 11/19/2022]
Abstract
Toxoplasma gondii is an intracellular parasite that causes severe neurologic and ocular disease in immune-compromised and congenitally infected individuals. There is no vaccine protective against human toxoplasmosis. Herein, immunization of L(d) mice with HF10 (HPGSVNEFDF) with palmitic acid moieties or a monophosphoryl lipid A derivative elicited potent IFN-gamma production from L(d)-restricted CD8(+) T cells in vitro and protected mice. CD8(+) T cell peptide epitopes from T. gondii dense granule proteins GRA 3, 6, 7, and Sag 1, immunogenic in humans for HLA-A02(+), HLA-A03(+), and HLA-B07(+) cells were identified. Since peptide repertoire presented by MHC class I molecules to CD8(+) T cells is shaped by endoplasmic reticulum-associated aminopeptidase (ERAAP), polymorphisms in the human ERAAP gene ERAP1 were studied and associate with susceptibility to human congenital toxoplasmosis (p<0.05). These results have important implications for vaccine development.
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MESH Headings
- Adjuvants, Immunologic/pharmacology
- Aminopeptidases/genetics
- Animals
- Antigens, Protozoan/immunology
- CD8-Positive T-Lymphocytes/immunology
- Epitopes, T-Lymphocyte/immunology
- Female
- Genetic Predisposition to Disease
- HLA-A Antigens/immunology
- HLA-B Antigens/immunology
- Humans
- Interferon-gamma/immunology
- Leukocytes, Mononuclear/immunology
- Lipopeptides/immunology
- Mice
- Mice, Inbred BALB C
- Mice, Transgenic
- Minor Histocompatibility Antigens
- Models, Molecular
- Polymorphism, Genetic
- Protozoan Proteins/immunology
- Protozoan Vaccines/immunology
- Toxoplasma/immunology
- Toxoplasmosis/genetics
- Toxoplasmosis/immunology
- Toxoplasmosis, Congenital/genetics
- Toxoplasmosis, Congenital/immunology
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Ge B, Pokholok DK, Kwan T, Grundberg E, Morcos L, Verlaan DJ, Le J, Koka V, Lam KCL, Gagné V, Dias J, Hoberman R, Montpetit A, Joly MM, Harvey EJ, Sinnett D, Beaulieu P, Hamon R, Graziani A, Dewar K, Harmsen E, Majewski J, Göring HHH, Naumova AK, Blanchette M, Gunderson KL, Pastinen T. Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet 2009; 41:1216-22. [PMID: 19838192 DOI: 10.1038/ng.473] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 08/24/2009] [Indexed: 12/15/2022]
Abstract
Cis-acting variants altering gene expression are a source of phenotypic differences. The cis-acting components of expression variation can be identified through the mapping of differences in allelic expression (AE), which is the measure of relative expression between two allelic transcripts. We generated a map of AE associated SNPs using quantitative measurements of AE on Illumina Human1M BeadChips. In 53 lymphoblastoid cell lines derived from donors of European descent, we identified common cis variants affecting 30% (2935/9751) of the measured RefSeq transcripts at 0.001 permutation significance. The pervasive influence of cis-regulatory variants, which explain 50% of population variation in AE, extend to full-length transcripts and their isoforms as well as to unannotated transcripts. These strong effects facilitate fine mapping of cis-regulatory SNPs, as demonstrated by dissection of heritable control of transcripts in the systemic lupus erythematosus-associated C8orf13-BLK region in chromosome 8. The dense collection of associations will facilitate large-scale isolation of cis-regulatory SNPs.
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Qu HQ, Jacob K, Fatet S, Ge B, Barnett D, Delattre O, Faury D, Montpetit A, Solomon L, Hauser P, Garami M, Bognar L, Hansely Z, Mio R, Farmer JP, Albrecht S, Polychronakos C, Hawkins C, Jabado N. Genome-wide profiling using single-nucleotide polymorphism arrays identifies novel chromosomal imbalances in pediatric glioblastomas. Neuro Oncol 2009; 12:153-63. [PMID: 20150382 DOI: 10.1093/neuonc/nop001] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Available data on genetic events in pediatric grade IV astrocytomas (glioblastoma [pGBM]) are scarce. This has traditionally been a major impediment in understanding the pathogenesis of this tumor and in developing ways for more effective management. Our aim is to chart DNA copy number aberrations (CNAs) and get insight into genetic pathways involved in pGBM. Using the Illumina Infinium Human-1 bead-chip-array (100K single-nucleotide polymorphisms [SNPs]), we genotyped 18 pediatric and 6 adult GBMs. Results were compared to BAC-array profiles harvested on 16 of the same pGBM, to an independent data set of 9 pediatric high-grade astrocytomas (HGAs) analyzed on Affymetrix 250K-SNP arrays, and to existing data sets on HGAs. CNAs were additionally validated by real-time qPCR in a set of genes in pGBM. Our results identify with nonrandom clustering of CNAs in several novel, previously not reported, genomic regions, suggesting that alterations in tumor suppressors and genes involved in the regulation of RNA processing and the cell cycle are major events in the pathogenesis of pGBM. Most regions were distinct from CNAs in aGBMs and show an unexpectedly low frequency of genetic amplification and homozygous deletions and a high frequency of loss of heterozygosity for a high-grade I rapidly dividing tumor. This first, complete, high-resolution profiling of the tumor cell genome fills an important gap in studies on pGBM. It ultimately guides the mapping of oncogenic networks unique to pGBM, identification of the related therapeutic predictors and targets, and development of more effective therapies. It further shows that, despite commonalities in a few CNAs, pGBM and aGBMs are two different diseases.
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