Michael E Talkowski

Publications (12)189.6 Total impact

• Article: Reciprocal deletion and duplication at 2q23.1 indicates a role for MBD5 in autism spectrum disorder.

  Sureni V Mullegama, Jill A Rosenfeld, Carmen Orellana, Bregje W M van Bon, Sara Halbach, Elena A Repnikova, Lauren Brick, Chumei Li, Lucie Dupuis, Monica Rosello, [......], Kory Keller, Jonathan Zonana, Stuart Schwartz, Robert E Pyatt, Darrel J Waggoner, Lisa G Shaffer, Angela E Lin, Bert B A de Vries, Roberto Mendoza-Londono, Sarah H Elsea
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  ABSTRACT: Copy number variations associated with abnormal gene dosage have an important role in the genetic etiology of many neurodevelopmental disorders, including intellectual disability (ID) and autism. We hypothesize that the chromosome 2q23.1 region encompassing MBD5 is a dosage-dependent region, wherein deletion or duplication results in altered gene dosage. We previously established the 2q23.1 microdeletion syndrome and report herein 23 individuals with 2q23.1 duplications, thus establishing a complementary duplication syndrome. The observed phenotype includes ID, language impairments, infantile hypotonia and gross motor delay, behavioral problems, autistic features, dysmorphic facial features (pinnae anomalies, arched eyebrows, prominent nose, small chin, thin upper lip), and minor digital anomalies (fifth finger clinodactyly and large broad first toe). The microduplication size varies among all cases and ranges from 68 kb to 53.7 Mb, encompassing a region that includes MBD5, an important factor in methylation patterning and epigenetic regulation. We previously reported that haploinsufficiency of MBD5 is the primary causal factor in 2q23.1 microdeletion syndrome and that mutations in MBD5 are associated with autism. In this study, we demonstrate that MBD5 is the only gene in common among all duplication cases and that overexpression of MBD5 is likely responsible for the core clinical features present in 2q23.1 microduplication syndrome. Phenotypic analyses suggest that 2q23.1 duplication results in a slightly less severe phenotype than the reciprocal deletion. The features associated with a deletion, mutation or duplication of MBD5 and the gene expression changes observed support MBD5 as a dosage-sensitive gene critical for normal development.European Journal of Human Genetics advance online publication, 1 May 2013; doi:10.1038/ejhg.2013.67.
  European journal of human genetics: EJHG 05/2013; · 3.56 Impact Factor
• Article: Lack of association of rare functional variants in TSC1/TSC2 genes with autism spectrum disorder.

  Samira Bahl, Colby Chiang, Roberta L Beauchamp, Benjamin M Neale, Mark J Daly, James F Gusella, Michael E Talkowski, Vijaya Ramesh
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  ABSTRACT: BACKGROUND: Autism spectrum disorder (ASD) is reported in 30 to 60% of patients with tuberous sclerosis complex (TSC) but shared genetic mechanisms that exist between TSC-associated ASD and idiopathic ASD have yet to be determined. Through the small G-protein Rheb, the TSC proteins, hamartin and tuberin, negatively regulate mammalian target of rapamycin complex 1 (mTORC1) signaling. It is well established that mTORC1 plays a pivotal role in neuronal translation and connectivity, so dysregulation of mTORC1 signaling could be a common feature in many ASDs. Pam, an E3 ubiquitin ligase, binds to TSC proteins and regulates mTORC1 signaling in the CNS, and the FBXO45-Pam ubiquitin ligase complex plays an essential role in neurodevelopment by regulating synapse formation and growth. Since mounting evidence has established autism as a disorder of the synapses, we tested whether rare genetic variants in TSC1, TSC2, MYCBP2, RHEB and FBXO45, genes that regulate mTORC1 signaling and/or play a role in synapse development and function, contribute to the pathogenesis of idiopathic ASD. METHODS: Exons and splice junctions of TSC1, TSC2, MYCBP2, RHEB and FBXO45 were resequenced for 300 ASD trios from the Simons Simplex Collection (SSC) using a pooled PCR amplification and next-generation sequencing strategy, targeted to the discovery of deleterious coding variation. These detected, potentially functional, variants were confirmed by Sanger sequencing of the individual samples comprising the pools in which they were identified. RESULTS: We identified a total of 23 missense variants in MYCBP2, TSC1 and TSC2. These variants exhibited a near equal distribution between the proband and parental pools, with no statistical excess in ASD cases (P > 0.05). All proband variants were inherited. No putative deleterious variants were confirmed in RHEB and FBXO45. Three intronic variants, identified as potential splice defects in MYCBP2 did not show aberrant splicing upon RNA assay. Overall, we did not find an over-representation of ASD causal variants in the genes studied to support them as contributors to autism susceptibility. CONCLUSIONS: We did not observe an enrichment of rare functional variants in TSC1 and TSC2 genes in our sample set of 300 trios.
  Molecular autism. 03/2013; 4(1):5.
• Article: Haploinsufficiency of KDM6A is associated with severe psychomotor retardation, global growth restriction, seizures and cleft palate.

  Amelia M Lindgren, Tatiana Hoyos, Michael E Talkowski, Carrie Hanscom, Ian Blumenthal, Colby Chiang, Carl Ernst, Shahrin Pereira, Zehra Ordulu, Carol Clericuzio, Joanne M Drautz, Jill A Rosenfeld, Lisa G Shaffer, Lea Velsher, Tania Pynn, Joris Vermeesch, David J Harris, James F Gusella, Eric C Liao, Cynthia C Morton
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  ABSTRACT: We describe a female subject (DGAP100) with a 46,X,t(X;5)(p11.3;q35.3)inv(5)(q35.3q35.1)dn, severe psychomotor retardation with hypotonia, global postnatal growth restriction, microcephaly, globally reduced cerebral volume, seizures, facial dysmorphia and cleft palate. Fluorescence in situ hybridization and whole-genome sequencing demonstrated that the X chromosome breakpoint disrupts KDM6A in the second intron. No genes were directly disrupted on chromosome 5. KDM6A is a histone 3 lysine 27 demethylase and a histone 3 lysine 4 methyltransferase. Expression of KDM6A is significantly reduced in DGAP100 lymphoblastoid cells compared to control samples. We identified nine additional cases with neurodevelopmental delay and various other features consistent with the DGAP100 phenotype with copy number variation encompassing KDM6A from microarray databases. We evaluated haploinsufficiency of kdm6a in a zebrafish model. kdm6a is expressed in the pharyngeal arches and ethmoid plate of the developing zebrafish, while a kdm6a morpholino knockdown exhibited craniofacial defects. We conclude KDM6A dosage regulation is associated with severe and diverse structural defects and developmental abnormalities.
  Human Genetics 01/2013; · 5.07 Impact Factor
• Article: Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities.

  Michael E Talkowski, Gilles Maussion, Liam Crapper, Jill A Rosenfeld, Ian Blumenthal, Carrie Hanscom, Colby Chiang, Amelia Lindgren, Shahrin Pereira, Douglas Ruderfer, [......], Pamela Sklar, Shaun Purcell, Manolis Kellis, Stuart Schwartz, Lisa G Shaffer, Marvin R Natowicz, Yiping Shen, Cynthia C Morton, James F Gusella, Carl Ernst
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  ABSTRACT: Large intergenic noncoding (linc) RNAs represent a newly described class of ribonucleic acid whose importance in human disease remains undefined. We identified a severely developmentally delayed 16-year-old female with karyotype 46,XX,t(2;11)(p25.1;p15.1)dn in the absence of clinically significant copy number variants (CNVs). DNA capture followed by next-generation sequencing of the translocation breakpoints revealed disruption of a single noncoding gene on chromosome 2, LINC00299, whose RNA product is expressed in all tissues measured, but most abundantly in brain. Among a series of additional, unrelated subjects referred for clinical diagnostic testing who showed CNV affecting this locus, we identified four with exon-crossing deletions in association with neurodevelopmental abnormalities. No disruption of the LINC00299 coding sequence was seen in almost 14,000 control subjects. Together, these subjects with disruption of LINC00299 implicate this particular noncoding RNA in brain development and raise the possibility that, as a class, abnormalities of lincRNAs may play a significant role in human developmental disorders.
  The American Journal of Human Genetics 12/2012; 91(6):1128-34. · 10.60 Impact Factor
• Article: Clinical Diagnosis by Whole-Genome Sequencing of a Prenatal Sample.

  Michael E Talkowski, Zehra Ordulu, Vamsee Pillalamarri, Carol B Benson, Ian Blumenthal, Susan Connolly, Carrie Hanscom, Naveed Hussain, Shahrin Pereira, Jonathan Picker, Jill A Rosenfeld, Lisa G Shaffer, Louise E Wilkins-Haug, James F Gusella, Cynthia C Morton
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  ABSTRACT: Conventional cytogenetic testing offers low-resolution detection of balanced karyotypic abnormalities but cannot provide the precise, gene-level knowledge required to predict outcomes. The use of high-resolution whole-genome deep sequencing is currently impractical for the purpose of routine clinical care. We show here that whole-genome "jumping libraries" can offer an immediately applicable, nucleotide-level complement to conventional genetic diagnostics within a time frame that allows for clinical action. We performed large-insert sequencing of DNA extracted from amniotic-fluid cells with a balanced de novo translocation. The amniotic-fluid sample was from a patient in the third trimester of pregnancy who underwent amniocentesis because of severe polyhydramnios after multiple fetal anomalies had been detected on ultrasonography. Using a 13-day sequence and analysis pipeline, we discovered direct disruption of CHD7, a causal locus in the CHARGE syndrome (coloboma of the eye, heart anomaly, atresia of the choanae, retardation, and genital and ear anomalies). Clinical findings at birth were consistent with the CHARGE syndrome, a diagnosis that could not have been reliably inferred from the cytogenetic breakpoint. This case study illustrates the potential power of customized whole-genome jumping libraries when used to augment prenatal karyotyping.
  New England Journal of Medicine 12/2012; 367(23):2226-2232. · 53.30 Impact Factor
• Article: Highly Penetrant Alterations of a Critical Region Including BDNF in Human Psychopathology and Obesity.

  Carl Ernst, Christian R Marshall, Yiping Shen, Kay Metcalfe, Jill Rosenfeld, Jennelle C Hodge, Alcy Torres, Ian Blumenthal, Colby Chiang, Vamsee Pillalamarri, [......], David J Harris, Emanuelle Lemyre, Bai-Lin Wu, Dimitri J Stavropoulos, Michael T Geraghty, Lisa G Shaffer, Cynthia C Morton, Stephen W Scherer, James F Gusella, Michael E Talkowski
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  ABSTRACT: CONTEXT Brain-derived neurotrophic factor (BDNF) is suspected of being a causative factor in psychiatric disorders based on case reports or studies involving large structural anomalies. OBJECTIVE To determine the involvement of BDNF in human psychopathology. DESIGN Case-control study. SETTING Microarray-based comparative genomic hybridization data from 7 molecular diagnostic centers including 38 550 affected subjects and 28 705 unaffected subjects. PATIENTS Subjects referred to diagnostic screening centers for microarray-based comparative genomic hybridization for physical or cognitive impairment. MAIN OUTCOME MEASURES Genomic copy number gains and losses. RESULTS We report 5 individuals with psychopathology and genomic deletion of a critical region including BDNF. The defined critical region was never disrupted in control subjects or diagnostic cases without developmental abnormalities. CONCLUSION Hemizygosity of the BDNF region contributes to variable psychiatric phenotypes including anxiety, behavioral, and mood disorders.
  Archives of general psychiatry 10/2012; · 12.26 Impact Factor
• Article: Translocations disrupting PHF21A in the Potocki-Shaffer-syndrome region are associated with intellectual disability and craniofacial anomalies.

  Hyung-Goo Kim, Hyun-Taek Kim, Natalia T Leach, Fei Lan, Reinhard Ullmann, Asli Silahtaroglu, Ingo Kurth, Anja Nowka, Ihn Sik Seong, Yiping Shen, [......], Hans-Hilger Ropers, Lisa G Shaffer, Kerstin Kutsche, Lawrence C Layman, Niels Tommerup, Vera M Kalscheuer, Yang Shi, Cynthia C Morton, Cheol-Hee Kim, James F Gusella
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  ABSTRACT: Potocki-Shaffer syndrome (PSS) is a contiguous gene disorder due to the interstitial deletion of band p11.2 of chromosome 11 and is characterized by multiple exostoses, parietal foramina, intellectual disability (ID), and craniofacial anomalies (CFAs). Despite the identification of individual genes responsible for multiple exostoses and parietal foramina in PSS, the identity of the gene(s) associated with the ID and CFA phenotypes has remained elusive. Through characterization of independent subjects with balanced translocations and supportive comparative deletion mapping of PSS subjects, we have uncovered evidence that the ID and CFA phenotypes are both caused by haploinsufficiency of a single gene, PHF21A, at 11p11.2. PHF21A encodes a plant homeodomain finger protein whose murine and zebrafish orthologs are both expressed in a manner consistent with a function in neurofacial and craniofacial development, and suppression of the latter led to both craniofacial abnormalities and neuronal apoptosis. Along with lysine-specific demethylase 1 (LSD1), PHF21A, also known as BHC80, is a component of the BRAF-histone deacetylase complex that represses target-gene transcription. In lymphoblastoid cell lines from two translocation subjects in whom PHF21A was directly disrupted by the respective breakpoints, we observed derepression of the neuronal gene SCN3A and reduced LSD1 occupancy at the SCN3A promoter, supporting a direct functional consequence of PHF21A haploinsufficiency on transcriptional regulation. Our finding that disruption of PHF21A by translocations in the PSS region is associated with ID adds to the growing list of ID-associated genes that emphasize the critical role of transcriptional regulation and chromatin remodeling in normal brain development and cognitive function.
  The American Journal of Human Genetics 07/2012; 91(1):56-72. · 10.60 Impact Factor
• Article: Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries.

  Michael E Talkowski, Jill A Rosenfeld, Ian Blumenthal, Vamsee Pillalamarri, Colby Chiang, Adrian Heilbut, Carl Ernst, Carrie Hanscom, Elizabeth Rossin, Amelia M Lindgren, [......], Bradley Quade, Kasper Lage, Judith Miles, Bai-Lin Wu, Yiping Shen, Benjamin Neale, Lisa G Shaffer, Mark J Daly, Cynthia C Morton, James F Gusella
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  ABSTRACT: Balanced chromosomal abnormalities (BCAs) represent a relatively untapped reservoir of single-gene disruptions in neurodevelopmental disorders (NDDs). We sequenced BCAs in patients with autism or related NDDs, revealing disruption of 33 loci in four general categories: (1) genes previously associated with abnormal neurodevelopment (e.g., AUTS2, FOXP1, and CDKL5), (2) single-gene contributors to microdeletion syndromes (MBD5, SATB2, EHMT1, and SNURF-SNRPN), (3) novel risk loci (e.g., CHD8, KIRREL3, and ZNF507), and (4) genes associated with later-onset psychiatric disorders (e.g., TCF4, ZNF804A, PDE10A, GRIN2B, and ANK3). We also discovered among neurodevelopmental cases a profoundly increased burden of copy-number variants from these 33 loci and a significant enrichment of polygenic risk alleles from genome-wide association studies of autism and schizophrenia. Our findings suggest a polygenic risk model of autism and reveal that some neurodevelopmental genes are sensitive to perturbation by multiple mutational mechanisms, leading to variable phenotypic outcomes that manifest at different life stages.
  Cell 04/2012; 149(3):525-37. · 32.40 Impact Factor
• Article: Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration.

  Colby Chiang, Jessie C Jacobsen, Carl Ernst, Carrie Hanscom, Adrian Heilbut, Ian Blumenthal, Ryan E Mills, Andrew Kirby, Amelia M Lindgren, Skye R Rudiger, [......], Ira M Hall, Yiping Shen, Toshiro K Ohsumi, Mark L Borowsky, Mark J Daly, Charles Lee, Cynthia C Morton, Marcy E MacDonald, James F Gusella, Michael E Talkowski
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  ABSTRACT: We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not unique to cancer cells but also occurs in the germline, where it can resolve to a relatively balanced state with frequent inversions. We detected a high incidence of complex rearrangements (19.2%) and substantially less reliance on microhomology (31%) than previously observed in benign copy-number variants (CNVs). We compared these results to experimentally generated DNA breakage-repair by sequencing seven transgenic animals, revealing extensive rearrangement of the transgene and host genome with similar complexity to human germline alterations. Inversion was the most common rearrangement, suggesting that a combined mechanism involving template switching and non-homologous repair mediates the formation of balanced complex rearrangements that are viable, stably replicated and transmitted unaltered to subsequent generations.
  Nature Genetics 03/2012; 44(4):390-7, S1. · 35.53 Impact Factor
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  Available from: Corrado Romano

  Article: Assessment of 2q23.1 microdeletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder.

  Michael E Talkowski, Sureni V Mullegama, Jill A Rosenfeld, Bregje W M van Bon, Yiping Shen, Elena A Repnikova, Julie Gastier-Foster, Devon Lamb Thrush, Sekar Kathiresan, Douglas M Ruderfer, [......], Margot I Van Allen, Aditi Parikh, Lilei Zhang, Bai-Lin Wu, Robert E Pyatt, Stuart Schwartz, Lisa G Shaffer, Bert B A de Vries, James F Gusella, Sarah H Elsea
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  ABSTRACT: Persons with neurodevelopmental disorders or autism spectrum disorder (ASD) often harbor chromosomal microdeletions, yet the individual genetic contributors within these regions have not been systematically evaluated. We established a consortium of clinical diagnostic and research laboratories to accumulate a large cohort with genetic alterations of chromosomal region 2q23.1 and acquired 65 subjects with microdeletion or translocation. We sequenced translocation breakpoints; aligned microdeletions to determine the critical region; assessed effects on mRNA expression; and examined medical records, photos, and clinical evaluations. We identified a single gene, methyl-CpG-binding domain 5 (MBD5), as the only locus that defined the critical region. Partial or complete deletion of MBD5 was associated with haploinsufficiency of mRNA expression, intellectual disability, epilepsy, and autistic features. Fourteen alterations, including partial deletions of noncoding regions not typically captured or considered pathogenic by current diagnostic screening, disrupted MBD5 alone. Expression profiles and clinical characteristics were largely indistinguishable between MBD5-specific alteration and deletion of the entire 2q23.1 interval. No copy-number alterations of MBD5 were observed in 7878 controls, suggesting MBD5 alterations are highly penetrant. We surveyed MBD5 coding variations among 747 ASD subjects compared to 2043 non-ASD subjects analyzed by whole-exome sequencing and detected an association with a highly conserved methyl-CpG-binding domain missense variant, p.79Gly>Glu (c.236G>A) (p = 0.012). These results suggest that genetic alterations of MBD5 cause features of 2q23.1 microdeletion syndrome and that this epigenetic regulator significantly contributes to ASD risk, warranting further consideration in research and clinical diagnostic screening and highlighting the importance of chromatin remodeling in the etiology of these complex disorders.
  The American Journal of Human Genetics 10/2011; 89(4):551-63. · 10.60 Impact Factor
• Article: The cell adhesion gene PVRL3 is associated with congenital ocular defects.

  Salil A Lachke, Anne W Higgins, Maiko Inagaki, Irfan Saadi, Qiongchao Xi, Michelle Long, Bradley J Quade, Michael E Talkowski, James F Gusella, Atsuko Fujimoto, Michael L Robinson, Ying Yang, Quynh T Duong, Irit Shapira, Benny Motro, Jun Miyoshi, Yoshimi Takai, Cynthia C Morton, Richard L Maas
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  ABSTRACT: We describe a male patient (patient DGAP113) with a balanced translocation, 46,XY,t(1;3)(q31.3;q13.13), severe bilateral congenital cataracts, CNS abnormalities and mild developmental delay. Fluorescence in situ hybridization (FISH) and suppression PCR demonstrated that the chromosome 3 breakpoint lies ~515 kb upstream of the PVRL3 gene, while the chromosome 1 breakpoint lies ~50 kb upstream of the NEK7 gene. Despite the fact that NEK7 is closer to a translocation breakpoint than PVRL3, NEK7 transcript levels are unaltered in patient DGAP113 lymphoblastoid cells and Nek7-deficient mice exhibit no detectable ocular phenotype. In contrast, the expression of PVRL3, which encodes the cell adhesion protein Nectin 3, is significantly reduced in patient DGAP113 lymphoblastoid cells, likely due to a position effect caused by the chromosomal translocation. Nectin 3 is expressed in the mouse embryonic ciliary body and lens. Moreover, Pvrl3 knockout mice as well as a spontaneous mouse mutant ari (anterior retinal inversion), that maps to the Pvrl3 locus, exhibit lens and other ocular defects involving the ciliary body. Collectively, these data identify PVRL3 as a critical gene involved in a Nectin-mediated cell-cell adhesion mechanism in human ocular development.
  Human Genetics 07/2011; 131(2):235-50. · 5.07 Impact Factor
• Article: Next-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research.

  Michael E Talkowski, Carl Ernst, Adrian Heilbut, Colby Chiang, Carrie Hanscom, Amelia Lindgren, Andrew Kirby, Shangtao Liu, Bhavana Muddukrishna, Toshiro K Ohsumi, Yiping Shen, Mark Borowsky, Mark J Daly, Cynthia C Morton, James F Gusella
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  ABSTRACT: The contribution of balanced chromosomal rearrangements to complex disorders remains unclear because they are not detected routinely by genome-wide microarrays and clinical localization is imprecise. Failure to consider these events bypasses a potentially powerful complement to single nucleotide polymorphism and copy-number association approaches to complex disorders, where much of the heritability remains unexplained. To capitalize on this genetic resource, we have applied optimized sequencing and analysis strategies to test whether these potentially high-impact variants can be mapped at reasonable cost and throughput. By using a whole-genome multiplexing strategy, rearrangement breakpoints could be delineated at a fraction of the cost of standard sequencing. For rearrangements already mapped regionally by karyotyping and fluorescence in situ hybridization, a targeted approach enabled capture and sequencing of multiple breakpoints simultaneously. Importantly, this strategy permitted capture and unique alignment of up to 97% of repeat-masked sequences in the targeted regions. Genome-wide analyses estimate that only 3.7% of bases should be routinely omitted from genomic DNA capture experiments. Illustrating the power of these approaches, the rearrangement breakpoints were rapidly defined to base pair resolution and revealed unexpected sequence complexity, such as co-occurrence of inversion and translocation as an underlying feature of karyotypically balanced alterations. These findings have implications ranging from genome annotation to de novo assemblies and could enable sequencing screens for structural variations at a cost comparable to that of microarrays in standard clinical practice.
  The American Journal of Human Genetics 04/2011; 88(4):469-81. · 10.60 Impact Factor