Browsing by Author "Lupski, James R."

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    Correction to: De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome
    (Biomed Central, 2019-03-25) Vetrini, Francesco; McKee, Shane; Rosenfeld, Jill A.; Suri, Mohnish; Lewis, Andrea M.; Nugent, Kimberly Margaret; Roeder, Elizabeth; Littlejohn, Rebecca O.; Holder, Sue; Zhu, Wenmiao; Alaimo, Joseph T.; Graham, Brett; Harris, Jill M.; Gibson, James B.; Pastore, Matthew; McBride, Kim L.; Komara, Makanko; Al-Gazali, Lihadh; Al Shamsi, Aisha; Fanning, Elizabeth A.; Wierenga, Klaas J.; Scott, Daryl A.; Ben-Neriah, Ziva; Meiner, Vardiella; Cassuto, Hanoch; Elpeleg, Orly; Lloyd Holder Jr, J.; Burrage, Lindsay C.; Seaver, Laurie H.; Van Maldergem, Lionel; Mahida, Sonal; Soul, Janet S.; Marlatt, Margaret; Matyakhina, Ludmila; Vogt, Julie; Gold, June-Anne; Park, Soo-Mi; Varghese, Vinod; Lampe, Anne K.; Kumar, Ajith; Lees, Melissa; Holder-Espinasse, Muriel; McConnell, Vivienne; Bernhard, Birgitta; Blair, Ed; Harrison, Victoria; Muzny, Donna M.; Gibbs, Richard A.; Elsea, Sarah H.; Posey, Jennifer E.; Bi, Weimin; Lalani, Seema; Xia, Fan; Yang, Yaping; Eng, Christine M.; Lupski, James R.; Liu, Pengfei; Medical and Molecular Genetics, School of Medicine
    It was highlighted that the original article [1] contained a typographical error in the Results section. Subject 17 was incorrectly cited as Subject 1. This Correction article shows the revised statement. The original article has been updated.
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    Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome
    (Elsevier, 2021-11) Weerts, Marjolein J.A.; Lanko, Kristina; Guzmán-Vega, Francisco J.; Jackson, Adam; Ramakrishnan, Reshmi; Cardona-Londoño, Kelly J.; Peña-Guerra, Karla A.; van Bever, Yolande; van Paassen, Barbara W.; Kievit, Anneke; van Slegtenhorst, Marjon; Allen, Nicholas M.; Kehoe, Caroline M.; Robinson, Hannah K.; Pang, Lewis; Banu, Selina H.; Zaman, Mashaya; Efthymiou, Stephanie; Houlden, Henry; Järvelä, Irma; Lauronen, Leena; Määttä, Tuomo; Schrauwen, Isabelle; Leal, Suzanne M.; Ruivenkamp, Claudia A.L.; Barge-Schaapveld, Daniela Q.C.M.; Peeters-Scholte, Cacha M.P.C.D.; Galehdari, Hamid; Mazaheri, Neda; Sisodiya, Sanjay M.; Harrison, Victoria; Sun, Angela; Thies, Jenny; Pedroza, Luis Alberto; Lara-Taranchenko, Yana; Chinn, Ivan K.; Lupski, James R.; Garza-Flores, Alexandra; McGlothlin, Jeffery; Yang, Lin; Huang, Shaoping; Wang, Xiaodong; Jewett, Tamison; Rosso, Gretchen; Lin, Xi; Mohammed, Shehla; Merritt, J. Lawrence, II.; Mirzaa, Ghayda M.; Timms, Andrew E.; Scheck, Joshua; Elting, Mariet W.; Polstra, Abeltje M.; Schenck, Lauren; Ruzhnikov, Maura R.Z.; Vetro, Annalisa; Montomoli, Martino; Guerrini, Renzo; Koboldt, Daniel C.; Mihalic Mosher, Theresa; Pastore, Matthew T.; McBride, Kim L.; Peng, Jing; Pan, Zou; Willemsen, Marjolein; Koning, Susanne; Turnpenny, Peter D.; de Vries, Bert B.A.; Gilissen, Christian; Pfundt, Rolph; Lees, Melissa; Braddock, Stephen R.; Klemp, Kara C.; Vansenne, Fleur; van Gijn, Marielle E.; Quindipan, Catherine; Deardorff, Matthew A.; Hamm, J. Austin; Putnam, Abbey M.; Baud, Rebecca; Walsh, Laurence; Lynch, Sally A.; Baptista, Julia; Person, Richard E.; Monaghan, Kristin G.; Crunk, Amy; Keller-Ramey, Jennifer; Reich, Adi; Elloumi, Houda Zghal; Alders, Marielle; Kerkhof, Jennifer; McConkey, Haley; Haghshenas, Sadegheh; Maroofian, Reza; Sadikovic, Bekim; Banka, Siddharth; Arold, Stefan T.; Barakat, Tahsin Stefan; Medical and Molecular Genetics, School of Medicine
    Purpose: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort. Methods: We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays. Results: Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants. Conclusion: Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome.
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    DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders
    (Elsevier, 2025) Lessel, Ivana; Baresic, Anja; Chinn, Ivan K.; May, Jonathan; Goenka, Anu; Chandler, Kate E.; Posey, Jennifer E.; Afenjar, Alexandra; Averdunk, Luisa; Bedeschi, Maria Francesca; Besnard, Thomas; Brager, Rae; Brick, Lauren; Brugger, Melanie; Brunet, Theresa; Byrne, Susan; de la Calle-Martín, Oscar; Capra, Valeria; Cardenas, Paul; Chappé, Céline; Chong, Hey J.; Cogne, Benjamin; Conboy, Erin; Cope, Heidi; Courtin, Thomas; Deb, Wallid; Dilena, Robertino; Dubourg, Christèle; Elgizouli, Magdeldin; Fernandes, Erica; Fitzgerald, Kristi K.; Gangi, Silvana; George-Abraham, Jaya K.; Gucsavas-Calikoglu, Muge; Haack, Tobias B.; Hadonou, Medard; Hanker, Britta; Hüning, Irina; Iascone, Maria; Isidor, Bertrand; Järvelä, Irma; Jin, Jay J.; Jorge, Alexander A. L.; Josifova, Dragana; Kalinauskiene, Ruta; Kamsteeg, Erik-Jan; Keren, Boris; Kessler, Elena; Kölbel, Heike; Kozenko, Mariya; Kubisch, Christian; Kuechler, Alma; Leal, Suzanne M.; Leppälä, Juha; Luu, Sharon M.; Lyon, Gholson J.; Madan-Khetarpal, Suneeta; Mancardi, Margherita; Marchi, Elaine; Mehta, Lakshmi; Menendez, Beatriz; Morel, Chantal F.; Moyer Harasink, Sue; Nevay, Dayna-Lynn; Nigro, Vincenzo; Odent, Sylvie; Oegema, Renske; Pappas, John; Pastore, Matthew T.; Perilla-Young, Yezmin; Platzer, Konrad; Powell-Hamilton, Nina; Rabin, Rachel; Rekab, Aisha; Rezende, Raissa C.; Robert, Leema; Romano, Ferruccio; Scala, Marcello; Poths, Karin; Schrauwen, Isabelle; Sebastian, Jessica; Short, John; Sidlow, Richard; Sullivan, Jennifer; Szakszon, Katalin; Tan, Queenie K. G.; Undiagnosed Diseases Network; Wagner, Matias; Wieczorek, Dagmar; Yuan, Bo; Maeding, Nicole; Strunk, Dirk; Begtrup, Amber; Banka, Siddharth; Lupski, James R.; Tolosa, Eva; Lessel, Davor; Medical and Molecular Genetics, School of Medicine
    BCL11B is a Cys2-His2 zinc-finger (C2H2-ZnF) domain-containing, DNA-binding, transcription factor with established roles in the development of various organs and tissues, primarily the immune and nervous systems. BCL11B germline variants have been associated with a variety of developmental syndromes. However, genotype-phenotype correlations along with pathophysiologic mechanisms of selected variants mostly remain elusive. To dissect these, we performed genotype-phenotype correlations of 92 affected individuals harboring a pathogenic or likely pathogenic BCL11B variant, followed by immune phenotyping, analysis of chromatin immunoprecipitation DNA-sequencing data, dual-luciferase reporter assays, and molecular modeling. These integrative analyses enabled us to define three clinical subtypes of BCL11B-related disorders. It is likely that gene-disruptive BCL11B variants and missense variants affecting zinc-binding cysteine and histidine residues cause mild to moderate neurodevelopmental delay with increased propensity for behavioral and dental anomalies, allergies and asthma, and reduced type 2 innate lymphoid cells. Missense variants within C2H2-ZnF DNA-contacting α helices cause highly variable clinical presentations ranging from multisystem anomalies with demise in the first years of life to late-onset, hyperkinetic movement disorder with poor fine motor skills. Those not in direct DNA contact cause a milder phenotype through reduced, target-specific transcriptional activity. However, missense variants affecting C2H2-ZnFs, DNA binding, and "specificity residues" impair BCL11B transcriptional activity in a target-specific, dominant-negative manner along with aberrant regulation of alternative DNA targets, resulting in more severe and unpredictable clinical outcomes. Taken together, we suggest that the phenotypic severity and variability is largely dependent on the DNA-binding affinity and specificity of altered BCL11B proteins.
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    Evidence for replicative mechanism in a CHD7 rearrangement in a patient with CHARGE syndrome
    (Wiley, 2013-12) Vatta, Matteo; Niu, Zhiyv; Lupski, James R.; Putnam, Philip; Spoonamore, Katherine G.; Fang, Ping; Eng, Christine M.; Willis, Alecia S.; Medical & Molecular Genetics, School of Medicine
    Haploinsufficiency of CHD7 (OMIM# 608892) is known to cause CHARGE syndrome (OMIM# 214800). Molecular testing supports a definitive diagnosis in approximately 65-70% of cases. Most CHD7 mutations arise de novo, and no mutations affecting exon-7 have been reported to date. We report on an 8-year-old girl diagnosed with CHARGE syndrome that was referred to our laboratory for comprehensive CHD7 gene screening. Genomic DNA from the subject with a suspected diagnosis of CHARGE was isolated from peripheral blood lymphocytes and comprehensive Sanger sequencing, along with deletion/duplication analysis of the CHD7 gene using multiplex ligation-dependent probe amplification (MLPA), was performed. MLPA analysis identified a reduced single probe signal for exon-7 of the CHD7 gene consistent with potential heterozygous deletion. Long-range PCR breakpoint analysis identified a complex genomic rearrangement (CGR) leading to the deletion of exon-7 and breakpoints consistent with a replicative mechanism such as fork stalling and template switching (FoSTeS) or microhomology-mediated break-induced replication (MMBIR). Taken together this represents the first evidence for a CHD7 intragenic CGR in a patient with CHARGE syndrome leading to what appears to be also the first report of a mutation specifically disrupting exon-7. Although likely rare, CGR may represent an overlooked mechanism in subjects with CHARGE syndrome that can be missed by current sequencing and dosage assays.
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    Genetic architecture of laterality defects revealed by whole exome sequencing
    (Springer Nature, 2019-04) Li, Alexander H.; Hanchard, Neil A.; Azamian, Mahshid; D’Alessandro, Lisa C. A.; Coban-Akdemir, Zeynep; Lopez, Keila N.; Hall, Nancy J.; Dickerson, Heather; Nicosia, Annarita; Fernbach, Susan; Boone, Philip M.; Gambin, Tomaz; Karaca, Ender; Gu, Shen; Yuan, Bo; Jhangiani, Shalini N.; Doddapaneni, HarshaVardhan; Hu, Jianhong; Dinh, Huyen; Jayaseelan, Joy; Muzny, Donna; Lalani, Seema; Towbin, Jeffrey; Penny, Daniel; Fraser, Charles; Martin, James; Lupski, James R.; Gibbs, Richard A.; Boerwinkle, Eric; Ware, Stephanie M.; Belmont, John W.; Pediatrics, School of Medicine
    Aberrant left-right patterning in the developing human embryo can lead to a broad spectrum of congenital malformations. The causes of most laterality defects are not known, with variants in established genes accounting for <20% of cases. We sought to characterize the genetic spectrum of these conditions by performing whole-exome sequencing of 323 unrelated laterality cases. We investigated the role of rare, predicted-damaging variation in 1726 putative laterality candidate genes derived from model organisms, pathway analyses, and human phenotypes. We also evaluated the contribution of homo/hemizygous exon deletions and gene-based burden of rare variation. A total of 28 candidate variants (26 rare predicted-damaging variants and 2 hemizygous deletions) were identified, including variants in genes known to cause heterotaxy and primary ciliary dyskinesia (ACVR2B, NODAL, ZIC3, DNAI1, DNAH5, HYDIN, MMP21), and genes without a human phenotype association, but with prior evidence for a role in embryonic laterality or cardiac development. Sanger validation of the latter variants in probands and their parents revealed no de novo variants, but apparent transmitted heterozygous (ROCK2, ISL1, SMAD2), and hemizygous (RAI2, RIPPLY1) variant patterns. Collectively, these variants account for 7.1% of our study subjects. We also observe evidence for an excess burden of rare, predicted loss-of-function variation in PXDNL and BMS1- two genes relevant to the broader laterality phenotype. These findings highlight potential new genes in the development of laterality defects, and suggest extensive locus heterogeneity and complex genetic models in this class of birth defects.
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    Genitourinary Defects Associated with Genomic Deletions in 2p15 Encompassing OTX1
    (Public Library of Science, 2014-09-09) Jorgez, Carolina J.; Rosenfeld, Jill A.; Wilken, Nathan R.; Vangapandu, Hima V.; Sahin, Aysegul; Pham, Dung; Carvalho, Claudia M. B.; Bandholz, Anne; Miller, Amanda; Weaver, David D.; Burton, Barbara; Babu, Deepti; Bamforth, John S.; Wilks, Timothy; Flynn, Daniel P.; Roeder, Elizabeth; Patel, Ankita; Cheung, Sau W.; Lupski, James R.; Lamb, Dolores J.; Medical and Molecular Genetics, School of Medicine
    Normal development of the genitourinary (GU) tract is a complex process that frequently goes awry. In male children the most frequent congenital GU anomalies are cryptorchidism (1-4%), hypospadias (1%) and micropenis (0.35%). Bladder exstrophy and epispadias complex (BEEC) (1∶47000) occurs less frequently but significantly impacts patients' lives. Array comparative genomic hybridization (aCGH) identified seven individuals with overlapping deletions in the 2p15 region (66.0 kb-5.6 Mb). Six of these patients have GU defects, while the remaining patient has no GU defect. These deletions encompass the transcription factor OTX1. Subjects 2-7 had large de novo CNVs (2.39-6.31 Mb) and exhibited features similar to those associated with the 2p15p16.1 and 2p15p14 microdeletion syndromes, including developmental delay, short stature, and variable GU defects. Subject-1 with BEEC had the smallest deletion (66 kb), which deleted only one copy of OTX1. Otx1-null mice have seizures, prepubescent transient growth retardation and gonadal defects. Two subjects have short stature, two have seizures, and six have GU defects, mainly affecting the external genitalia. The presence of GU defects in six patients in our cohort and eight of thirteen patients reported with deletions within 2p14p16.1 (two with deletion of OTX1) suggest that genes in 2p15 are important for GU development. Genitalia defects in these patients could result from the effect of OTX1 on pituitary hormone secretion or on the regulation of SHH signaling, which is crucial for development of the bladder and genitalia.
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    Lessons learned from additional research analyses of unsolved clinical exome cases
    (BioMed Central, 2017-03-21) Eldomery, Mohammad K.; Coban-Akdemir, Zeynep; Harel, Tamar; Rosenfeld, Jill A.; Gambin, Tomasz; Stray-Pedersen, Asbjørg; Küry, Sébastien; Mercier, Sandra; Lessel, Davor; Denecke, Jonas; Wiszniewski, Wojciech; Penney, Samantha; Liu, Pengfei; Bi, Weimin; Lalani, Seema R.; Schaaf, Christian P.; Wangler, Michael F.; Bacino, Carlos A.; Lewis, Richard Alan; Potocki, Lorraine; Graham, Brett H.; Belmont, John W.; Scaglia, Fernando; Orange, Jordan S.; Jhangiani, Shalini N.; Chiang, Theodore; Doddapaneni, Harsha; Hu, Jianhong; Muzny, Donna M.; Xia, Fan; Beaudet, Arthur L.; Boerwinkle, Eric; Eng, Christine M.; Plon, Sharon E.; Sutton, V. Reid; Gibbs, Richard A.; Posey, Jennifer E.; Yang, Yaping; Lupski, James R.; Department of Pathology and Laboratory Medicine, IU School of Medicine
    BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. RESULTS: Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). CONCLUSION: An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
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    MED27 Variants Cause Developmental Delay, Dystonia, and Cerebellar Hypoplasia
    (Wiley, 2021) Meng, Linyan; Isohanni, Pirjo; Shao, Yunru; Graham, Brett H.; Hickey, Scott E.; Brooks, Stephanie; Suomalainen, Anu; Joset, Pascal; Steindl, Katharina; Rauch, Anita; Hackenberg, Annette; High, Frances A.; Armstrong-Javors, Amy; Mencacci, Niccolò E.; Gonzàlez-Latapi, Paulina; Kamel, Walaa A.; Al-Hashel, Jasem Y.; Bustos, Bernabé I.; Hernandez, Alejandro V.; Krainc, Dimitri; Lubbe, Steven J.; Van Esch, Hilde; De Luca, Chiara; Ballon, Katleen; Ravelli, Claudia; Burglen, Lydie; Qebibo, Leila; Calame, Daniel G.; Mitani, Tadahiro; Marafi, Dana; Pehlivan, Davut; Saadi, Nebal W.; Sahin, Yavuz; Maroofian, Reza; Efthymiou, Stephanie; Houlden, Henry; Maqbool, Shazia; Rahman, Fatima; Gu, Shen; Posey, Jennifer E.; Lupski, James R.; Hunter, Jill V.; Wangler, Michael F.; Carroll, Christopher J.; Yang, Yaping; Medical and Molecular Genetics, School of Medicine
    The Mediator multiprotein complex functions as a regulator of RNA polymerase II-catalyzed gene transcription. In this study, exome sequencing detected biallelic putative disease-causing variants in MED27, encoding Mediator complex subunit 27, in 16 patients from 11 families with a novel neurodevelopmental syndrome. Patient phenotypes are highly homogeneous, including global developmental delay, intellectual disability, axial hypotonia with distal spasticity, dystonic movements, and cerebellar hypoplasia. Seizures and cataracts were noted in severely affected individuals. Identification of multiple patients with biallelic MED27 variants supports the critical role of MED27 in normal human neural development, particularly for the cerebellum.
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    Missense variants in TAF1 and developmental phenotypes: Challenges of determining pathogenicity
    (Wiley, 2019-10-23) Cheng, Hanyin; Capponi, Simona; Wakeling, Emma; Marchi, Elaine; Li, Quan; Zhao, Mengge; Weng, Chunhua; Piatek, Stefan G.; Ahlfors, Helena; Kleyner, Robert; Rope, Alan; Lumaka, Aimé; Lukusa, Prosper; Devriendt, Koenraad; Vermeesch, Joris; Posey, Jennifer E.; Palmer, Elizabeth E.; Murray, Lucinda; Leon, Eyby; Diaz, Jullianne; Worgan, Lisa; Mallawaarachchi, Amali; Vogt, Julie; de Munnik, Sonja A.; Dreyer, Lauren; Baynam, Gareth; Ewans, Lisa; Stark, Zornitza; Lunke, Sebastian; Gonçalves, Ana R.; Soares, Gabriela; Oliveira, Jorge; Fassi, Emily; Willing, Marcia; Waugh, Jeff L.; Faivre, Laurence; Riviere, Jean-Baptiste; Moutton, Sebastien; Mohammed, Shehla; Payne, Katelyn; Walsh, Laurence; Begtrup, Amber; Guillen Sacoto, Maria J.; Douglas, Ganka; Alexander, Nora; Buckley, Michael F.; Mark, Paul R.; Adès, Lesley C.; Sandaradura, Sarah A.; Lupski, James R.; Roscioli, Tony; Agrawal, Pankaj B.; Kline, Antonie D.; Wang, Kai; Timmers, T. Marc; Lyon, Gholson J.; Neurology, School of Medicine
    We recently described a new neurodevelopmental syndrome (TAF1/MRXS33 intellectual disability syndrome) (MIM# 300966) caused by pathogenic variants involving the X-linked gene TAF1, which participates in RNA polymerase II transcription. The initial study reported eleven families, and the syndrome was defined as presenting early in life with hypotonia, facial dysmorphia, and developmental delay that evolved into intellectual disability (ID) and/or autism spectrum disorder (ASD). We have now identified an additional 27 families through a genotype-first approach. Familial segregation analysis, clinical phenotyping, and bioinformatics were capitalized on to assess potential variant pathogenicity, and molecular modelling was performed for those variants falling within structurally characterized domains of TAF1. A novel phenotypic clustering approach was also applied, in which the phenotypes of affected individuals were classified using 51 standardized Human Phenotype Ontology (HPO) terms. Phenotypes associated with TAF1 variants show considerable pleiotropy and clinical variability, but prominent among previously unreported effects were brain morphological abnormalities, seizures, hearing loss, and heart malformations. Our allelic series broadens the phenotypic spectrum of TAF1/MRXS33 intellectual disability syndrome and the range of TAF1 molecular defects in humans. It also illustrates the challenges for determining the pathogenicity of inherited missense variants, particularly for genes mapping to chromosome X.
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    NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits
    (Cold Spring Harbor Laboratory, 2013) Dittwald, Piotr; Gambin, Tomasz; Szafranski, Przemyslaw; Li, Jian; Amato, Stephen; Divon, Michael Y.; Rodríguez Rojas, Lisa Ximena; Elton, Lindsay E.; Scott, Daryl A.; Schaaf, Christian P.; Torres-Martinez, Wilfredo; Stevens, Abby K.; Rosenfeld, Jill A.; Agadi, Satish; Francis, David; Kang, Sung-Hae L.; Breman, Amy; Lalani, Seema R.; Bacino, Carlos A.; Bi, Weimin; Milosavljevic, Aleksandar; Beaudet, Arthur L.; Patel, Ankita; Shaw, Chad A.; Lupski, James R.; Gambin, Anna; Cheung, Sau Wai; Stankiewicz, Pawel; Medical and Molecular Genetics, School of Medicine
    We delineated and analyzed directly oriented paralogous low-copy repeats (DP-LCRs) in the most recent version of the human haploid reference genome. The computationally defined DP-LCRs were cross-referenced with our chromosomal microarray analysis (CMA) database of 25,144 patients subjected to genome-wide assays. This computationally guided approach to the empirically derived large data set allowed us to investigate genomic rearrangement relative frequencies and identify new loci for recurrent nonallelic homologous recombination (NAHR)-mediated copy-number variants (CNVs). The most commonly observed recurrent CNVs were NPHP1 duplications (233), CHRNA7 duplications (175), and 22q11.21 deletions (DiGeorge/velocardiofacial syndrome, 166). In the ∼25% of CMA cases for which parental studies were available, we identified 190 de novo recurrent CNVs. In this group, the most frequently observed events were deletions of 22q11.21 (48), 16p11.2 (autism, 34), and 7q11.23 (Williams-Beuren syndrome, 11). Several features of DP-LCRs, including length, distance between NAHR substrate elements, DNA sequence identity (fraction matching), GC content, and concentration of the homologous recombination (HR) hot spot motif 5'-CCNCCNTNNCCNC-3', correlate with the frequencies of the recurrent CNVs events. Four novel adjacent DP-LCR-flanked and NAHR-prone regions, involving 2q12.2q13, were elucidated in association with novel genomic disorders. Our study quantitates genome architectural features responsible for NAHR-mediated genomic instability and further elucidates the role of NAHR in human disease.