The American Journal of Human Genetics

Publications in this journal

• Article: 2011 William Allan Award: development and evolution.

  John M Opitz
  The American Journal of Human Genetics 03/3012; 90(3):392-404.
• Article: 2011 introduction to Curt Stern Award.

  Aravinda Chakravarti
  The American Journal of Human Genetics 03/3012; 90(3):405-6.
• Article: 2011 Presidential Address: from classroom to courtroom to clinic-closing the gaps in human genetics education.

  Lynn B Jorde
  The American Journal of Human Genetics 03/3012; 90(3):387-9.
• Article: Haploinsufficiency of ARID1B, a member of the SWI/SNF-a chromatin-remodeling complex, is a frequent cause of intellectual disability.

  Juliane Hoyer, Arif B Ekici, Sabine Endele, Bernt Popp, Christiane Zweier, Antje Wiesener, Eva Wohlleber, Andreas Dufke, Eva Rossier, Corinna Petsch, Markus Zweier, Ina Göhring, Alexander M Zink, Gudrun Rappold, Evelin Schröck, Dagmar Wieczorek, Olaf Riess, Hartmut Engels, Anita Rauch, André Reis
  [show abstract] [hide abstract]
  ABSTRACT: Intellectual disability (ID) is a clinically and genetically heterogeneous common condition that remains etiologically unresolved in the majority of cases. Although several hundred diseased genes have been identified in X-linked, autosomal-recessive, or syndromic types of ID, the establishment of an etiological basis remains a difficult task in unspecific, sporadic cases. Just recently, de novo mutations in SYNGAP1, STXBP1, MEF2C, and GRIN2B were reported as relatively common causes of ID in such individuals. On the basis of a patient with severe ID and a 2.5 Mb microdeletion including ARID1B in chromosomal region 6q25, we performed mutational analysis in 887 unselected patients with unexplained ID. In this cohort, we found eight (0.9%) additional de novo nonsense or frameshift mutations predicted to cause haploinsufficiency. Our findings indicate that haploinsufficiency of ARID1B, a member of the SWI/SNF-A chromatin-remodeling complex, is a common cause of ID, and they add to the growing evidence that chromatin-remodeling defects are an important contributor to neurodevelopmental disorders.
  The American Journal of Human Genetics 03/3012; 90(3):565-72.
• Article: 2011 William Allan Award introduction: John M. Opitz.

  Maximilian Muenke
  The American Journal of Human Genetics 03/3012; 90(3):390-1.
• Article: 2011 Curt Stern Award address.

  David Altshuler
  The American Journal of Human Genetics 03/3012; 90(3):407-9.
• Article: Exome sequencing reveals mutations in TRPV3 as a cause of Olmsted syndrome.

  Zhimiao Lin, Quan Chen, Mingyang Lee, Xu Cao, Jie Zhang, Donglai Ma, Long Chen, Xiaoping Hu, Huijun Wang, Xiaowen Wang, [......], Xuanzhu Liu, Liping Guan, Yiquan Tang, Haizhen Yang, Ping Tu, Dingfang Bu, Xuejun Zhu, KeWei Wang, Ruoyu Li, Yong Yang
  [show abstract] [hide abstract]
  ABSTRACT: Olmsted syndrome (OS) is a rare congenital disorder characterized by palmoplantar and periorificial keratoderma, alopecia in most cases, and severe itching. The genetic basis for OS remained unidentified. Using whole-exome sequencing of case-parents trios, we have identified a de novo missense mutation in TRPV3 that produces p.Gly573Ser in an individual with OS. Nucleotide sequencing of five additional affected individuals also revealed missense mutations in TRPV3 (which produced p.Gly573Ser in three cases and p.Gly573Cys and p.Trp692Gly in one case each). Encoding a transient receptor potential vanilloid-3 cation channel, TRPV3 is primarily expressed in the skin, hair follicles, brain, and spinal cord. In transfected HEK293 cells expressing TRPV3 mutants, much larger inward currents were recorded, probably because of the constitutive opening of the mutants. These gain-of-function mutations might lead to elevated apoptosis of keratinocytes and consequent skin hyperkeratosis in the affected individuals. Our findings suggest that TRPV3 plays essential roles in skin keratinization, hair growth, and possibly itching sensation in humans and selectively targeting TRPV3 could provide therapeutic potential for keratinization or itching-related skin disorders.
  The American Journal of Human Genetics 03/3012; 90(3):558-64.
• Article: Infantile cerebellar-retinal degeneration associated with a mutation in mitochondrial aconitase, ACO2.

  Ronen Spiegel, Ophry Pines, Asaf Ta-Shma, Efrat Burak, Avraham Shaag, Jonatan Halvardson, Shimon Edvardson, Muhammad Mahajna, Shamir Zenvirt, Ann Saada, Stavit Shalev, Lars Feuk, Orly Elpeleg
  [show abstract] [hide abstract]
  ABSTRACT: Degeneration of the cerebrum, cerebellum, and retina in infancy is part of the clinical spectrum of lysosomal storage disorders, mitochondrial respiratory chain defects, carbohydrate glycosylation defects, and infantile neuroaxonal dystrophy. We studied eight individuals from two unrelated families who presented at 2-6 months of age with truncal hypotonia and athetosis, seizure disorder, and ophthalmologic abnormalities. Their course was characterized by failure to acquire developmental milestones and culminated in profound psychomotor retardation and progressive visual loss, including optic nerve and retinal atrophy. Despite their debilitating state, the disease was compatible with survival of up to 18 years. Laboratory investigations were normal, but the oxidation of glutamate by muscle mitochondria was slightly reduced. Serial brain MRI displayed progressive, prominent cerebellar atrophy accompanied by thinning of the corpus callosum, dysmyelination, and frontal and temporal cortical atrophy. Homozygosity mapping followed by whole-exome sequencing disclosed a Ser112Arg mutation in ACO2, encoding mitochondrial aconitase, a component of the Krebs cycle. Specific aconitase activity in the individuals' lymphoblasts was severely reduced. Under restrictive conditions, the mutant human ACO2 failed to complement a yeast ACO1 deletion strain, whereas the wild-type human ACO2 succeeded, indicating that this mutation is pathogenic. Thus, a defect in mitochondrial aconitase is associated with an infantile neurodegenerative disorder affecting mainly the cerebellum and retina. In the absence of noninvasive biomarkers, determination of the ACO2 sequence or of aconitase activity in lymphoblasts are warranted in similarly affected individuals, based on clinical and neuroradiologic grounds.
  The American Journal of Human Genetics 03/3012; 90(3):518-23.
• Article: Defective Initiation of Glycosaminoglycan Synthesis due to B3GALT6 Mutations Causes a Pleiotropic Ehlers-Danlos Syndrome-like Connective Tissue Disorder.

  Fransiska Malfait, Ariana Kariminejad, Tim Van Damme, Caroline Gauche, Delfien Syx, Faten Merhi-Soussi, Sandrine Gulberti, Sofie Symoens, Suzanne Vanhauwaert, Andy Willaert, Bita Bozorgmehr, Mohamad Hasan Kariminejad, Nazanin Ebrahimiadib, Ingrid Hausser, Ann Huysseune, Sylvie Fournel-Gigleux, Anne De Paepe
  [show abstract] [hide abstract]
  ABSTRACT: Proteoglycans are important components of cell plasma membranes and extracellular matrices of connective tissues. They consist of glycosaminoglycan chains attached to a core protein via a tetrasaccharide linkage, whereby the addition of the third residue is catalyzed by galactosyltransferase II (β3GalT6), encoded by B3GALT6. Homozygosity mapping and candidate gene sequence analysis in three independent families, presenting a severe autosomal-recessive connective tissue disorder characterized by skin fragility, delayed wound healing, joint hyperlaxity and contractures, muscle hypotonia, intellectual disability, and a spondyloepimetaphyseal dysplasia with bone fragility and severe kyphoscoliosis, identified biallelic B3GALT6 mutations, including homozygous missense mutations in family 1 (c.619G>C [p.Asp207His]) and family 3 (c.649G>A [p.Gly217Ser]) and compound heterozygous mutations in family 2 (c.323_344del [p.Ala108Glyfs(*)163], c.619G>C [p.Asp207His]). The phenotype overlaps with several recessive Ehlers-Danlos variants and spondyloepimetaphyseal dysplasia with joint hyperlaxity. Affected individuals' fibroblasts exhibited a large decrease in ability to prime glycosaminoglycan synthesis together with impaired glycanation of the small chondroitin/dermatan sulfate proteoglycan decorin, confirming β3GalT6 loss of function. Dermal electron microcopy disclosed abnormalities in collagen fibril organization, in line with the important regulatory role of decorin in this process. A strong reduction in heparan sulfate level was also observed, indicating that β3GalT6 deficiency alters synthesis of both main types of glycosaminoglycans. In vitro wound healing assay revealed a significant delay in fibroblasts from two index individuals, pointing to a role for glycosaminoglycan defect in impaired wound repair in vivo. Our study emphasizes a crucial role for β3GalT6 in multiple major developmental and pathophysiological processes.
  The American Journal of Human Genetics 05/2013;
• Article: Mutations in BICD2, which Encodes a Golgin and Important Motor Adaptor, Cause Congenital Autosomal-Dominant Spinal Muscular Atrophy.

  Kornelia Neveling, Lilian A Martinez-Carrera, Irmgard Hölker, Angelien Heister, Aad Verrips, Seyyed Mohsen Hosseini-Barkooie, Christian Gilissen, Sascha Vermeer, Maartje Pennings, Rowdy Meijer, [......], Sabine Rudnik-Schöneborn, Richard J Sinke, Klaus Zerres, R Brian Lowry, Henny H Lemmink, Lutz Garbes, Joris A Veltman, Helenius J Schelhaas, Hans Scheffer, Brunhilde Wirth
  [show abstract] [hide abstract]
  ABSTRACT: Spinal muscular atrophy (SMA) is a heterogeneous group of neuromuscular disorders caused by degeneration of lower motor neurons. Although functional loss of SMN1 is associated with autosomal-recessive childhood SMA, the genetic cause for most families affected by dominantly inherited SMA is unknown. Here, we identified pathogenic variants in bicaudal D homolog 2 (Drosophila) (BICD2) in three families afflicted with autosomal-dominant SMA. Affected individuals displayed congenital slowly progressive muscle weakness mainly of the lower limbs and congenital contractures. In a large Dutch family, linkage analysis identified a 9q22.3 locus in which exome sequencing uncovered c.320C>T (p.Ser107Leu) in BICD2. Sequencing of 23 additional families affected by dominant SMA led to the identification of pathogenic variants in one family from Canada (c.2108C>T [p.Thr703Met]) and one from the Netherlands (c.563A>C [p.Asn188Thr]). BICD2 is a golgin and motor-adaptor protein involved in Golgi dynamics and vesicular and mRNA transport. Transient transfection of HeLa cells with all three mutant BICD2 cDNAs caused massive Golgi fragmentation. This observation was even more prominent in primary fibroblasts from an individual harboring c.2108C>T (p.Thr703Met) (affecting the C-terminal coiled-coil domain) and slightly less evident in individuals with c.563A>C (p.Asn188Thr) (affecting the N-terminal coiled-coil domain). Furthermore, BICD2 levels were reduced in affected individuals and trapped within the fragmented Golgi. Previous studies have shown that Drosophila mutant BicD causes reduced larvae locomotion by impaired clathrin-mediated synaptic endocytosis in neuromuscular junctions. These data emphasize the relevance of BICD2 in synaptic-vesicle recycling and support the conclusion that BICD2 mutations cause congenital slowly progressive dominant SMA.
  The American Journal of Human Genetics 05/2013;
• Article: Molecular Defects in the Motor Adaptor BICD2 Cause Proximal Spinal Muscular Atrophy with Autosomal-Dominant Inheritance.

  Kristien Peeters, Ivan Litvinenko, Bob Asselbergh, Leonardo Almeida-Souza, Teodora Chamova, Thomas Geuens, Elke Ydens, Magdalena Zimoń, Joy Irobi, Els De Vriendt, Vicky De Winter, Tinne Ooms, Vincent Timmerman, Ivailo Tournev, Albena Jordanova
  [show abstract] [hide abstract]
  ABSTRACT: The most common form of spinal muscular atrophy (SMA) is a recessive disorder caused by deleterious SMN1 mutations in 5q13, whereas the genetic etiologies of non-5q SMA are very heterogeneous and largely remain to be elucidated. In a Bulgarian family affected by autosomal-dominant proximal SMA, we performed genome-wide linkage analysis and whole-exome sequencing and found a heterozygous de novo c.320C>T (p.Ser107Leu) mutation in bicaudal D homolog 2 (Drosophila) (BICD2). Further analysis of BICD2 in a cohort of 119 individuals with non-5q SMA identified a second de novo BICD2 mutation, c.2321A>G (p.Glu774Gly), in a simplex case. Detailed clinical and electrophysiological investigations revealed that both families are affected by a very similar disease course, characterized by early childhood onset, predominant involvement of lower extremities, and very slow disease progression. The amino acid substitutions are located in two interaction domains of BICD2, an adaptor protein linking the dynein molecular motor with its cargo. Our immunoprecipitation and localization experiments in HeLa and SH-SY5Y cells and affected individuals' lymphoblasts demonstrated that p.Ser107Leu causes increased dynein binding and thus leads to accumulation of BICD2 at the microtubule-organizing complex and Golgi fragmentation. In addition, the altered protein had a reduced colocalization with RAB6A, a regulator of vesicle trafficking between the Golgi and the endoplasmic reticulum. The interaction between p.Glu744Gly altered BICD2 and RAB6A was impaired, which also led to their reduced colocalization. Our study identifies BICD2 mutations as a cause of non-5q linked SMA and highlights the importance of dynein-mediated motility in motor neuron function in humans.
  The American Journal of Human Genetics 05/2013;
• Article: Mutations in B3GALT6, which Encodes a Glycosaminoglycan Linker Region Enzyme, Cause a Spectrum of Skeletal and Connective Tissue Disorders.

  Masahiro Nakajima, Shuji Mizumoto, Noriko Miyake, Ryo Kogawa, Aritoshi Iida, Hironori Ito, Hiroshi Kitoh, Aya Hirayama, Hiroshi Mitsubuchi, Osamu Miyazaki, [......], Shigehiko Watanabe, Ekkehart Lausch, Sheila Unger, Luisa Bonafé, Hirofumi Ohashi, Andrea Superti-Furga, Naomichi Matsumoto, Kazuyuki Sugahara, Gen Nishimura, Shiro Ikegawa
  [show abstract] [hide abstract]
  ABSTRACT: Proteoglycans (PGs) are a major component of the extracellular matrix in many tissues and function as structural and regulatory molecules. PGs are composed of core proteins and glycosaminoglycan (GAG) side chains. The biosynthesis of GAGs starts with the linker region that consists of four sugar residues and is followed by repeating disaccharide units. By exome sequencing, we found that B3GALT6 encoding an enzyme involved in the biosynthesis of the GAG linker region is responsible for a severe skeletal dysplasia, spondyloepimetaphyseal dysplasia with joint laxity type 1 (SEMD-JL1). B3GALT6 loss-of-function mutations were found in individuals with SEMD-JL1 from seven families. In a subsequent candidate gene study based on the phenotypic similarity, we found that B3GALT6 is also responsible for a connective tissue disease, Ehlers-Danlos syndrome (progeroid form). Recessive loss-of-function mutations in B3GALT6 result in a spectrum of disorders affecting a broad range of skeletal and connective tissues characterized by lax skin, muscle hypotonia, joint dislocation, and spinal deformity. The pleiotropic phenotypes of the disorders indicate that B3GALT6 plays a critical role in a wide range of biological processes in various tissues, including skin, bone, cartilage, tendon, and ligament.
  The American Journal of Human Genetics 05/2013;
• Article: Genome-wide Association Analysis for Multiple Continuous Secondary Phenotypes.

  Elizabeth D Schifano, Lin Li, David C Christiani, Xihong Lin
  [show abstract] [hide abstract]
  ABSTRACT: There is increasing interest in the joint analysis of multiple phenotypes in genome-wide association studies (GWASs), especially for the analysis of multiple secondary phenotypes in case-control studies and in detecting pleiotropic effects. Multiple phenotypes often measure the same underlying trait. By taking advantage of similarity across phenotypes, one could potentially gain statistical power in association analysis. Because continuous phenotypes are likely to be measured on different scales, we propose a scaled marginal model for testing and estimating the common effect of single-nucleotide polymorphism (SNP) on multiple secondary phenotypes in case-control studies. This approach improves power in comparison to individual phenotype analysis and traditional multivariate analysis when phenotypes are positively correlated and measure an underlying trait in the same direction (after transformation) by borrowing strength across outcomes with a one degree of freedom (1-DF) test and jointly estimating outcome-specific scales along with the SNP and covariate effects. To account for case-control ascertainment bias for the analysis of multiple secondary phenotypes, we propose weighted estimating equations for fitting scaled marginal models. This weighted estimating equation approach is robust to departures from normality of continuous multiple phenotypes and the misspecification of within-individual correlation among multiple phenotypes. Statistical power improves when the within-individual correlation is correctly specified. We perform simulation studies to show the proposed 1-DF common effect test outperforms several alternative methods. We apply the proposed method to investigate SNP associations with smoking behavior measured with multiple secondary smoking phenotypes in a lung cancer case-control GWAS and identify several SNPs of biological interest.
  The American Journal of Human Genetics 05/2013; 92(5):744-59.
• Article: eXclusion: Toward Integrating the X Chromosome in Genome-wide Association Analyses.

  Anastasia L Wise, Lin Gyi, Teri A Manolio
  [show abstract] [hide abstract]
  ABSTRACT: The X chromosome lags behind autosomal chromosomes in genome-wide association study (GWAS) findings. Indeed, the X chromosome is commonly excluded from GWAS analyses despite being assayed on all current GWAS microarray platforms. This raises the question: why are so few hits reported on the X chromosome? This commentary aims to examine this question through review of the current X chromosome results in the National Human Genome Research Institute Catalog of Published Genome-Wide Association Studies (NHGRI GWAS Catalog). It will also investigate commonly cited reasons for exclusion of the X chromosome from GWAS and review the tools currently available for X chromosome analysis. It will conclude with recommendations for incorporating X chromosome analyses in future studies.
  The American Journal of Human Genetics 05/2013; 92(5):643-7.
• Article: Weight loss after gastric bypass is associated with a variant at 15q26.1.

  Ida J Hatoum, Danielle M Greenawalt, Chris Cotsapas, Mark J Daly, Marc L Reitman, Lee M Kaplan
  [show abstract] [hide abstract]
  ABSTRACT: The amount of weight loss attained after Roux-en-Y gastric bypass (RYGB) surgery follows a wide and normal distribution, and recent evidence indicates that this weight loss is due to physiological, rather than mechanical, mechanisms. To identify potential genetic factors associated with weight loss after RYGB, we performed a genome-wide association study (GWAS) of 693 individuals undergoing RYGB and then replicated this analysis in an independent population of 327 individuals undergoing RYGB. We found that a 15q26.1 locus near ST8SIA2 and SLCO3A1 was significantly associated with weight loss after RYGB. Expression of ST8SIA2 in omental fat of these individuals at baseline was significantly associated with weight loss after RYGB. Gene expression analysis in RYGB and weight-matched, sham-operated (WMS) mice revealed that expression of St8sia2 and Slco3a1 was significantly altered in metabolically active tissues in RYGB-treated compared to WMS mice. These findings provide strong evidence for specific genetic influences on weight loss after RYGB and underscore the biological nature of the response to RYGB.
  The American Journal of Human Genetics 05/2013; 92(5):827-34.
• Article: Mutations in DARS Cause Hypomyelination with Brain Stem and Spinal Cord Involvement and Leg Spasticity.

  Ryan J Taft, Adeline Vanderver, Richard J Leventer, Stephen A Damiani, Cas Simons, Sean M Grimmond, David Miller, Johanna Schmidt, Paul J Lockhart, Kate Pope, [......], Monica Juneja, Ishwar C Verma, Prab Prabhakar, Susan Blaser, Julian Raiman, Petra J W Pouwels, Marianna R Bevova, Truus E M Abbink, Marjo S van der Knaap, Nicole I Wolf
  [show abstract] [hide abstract]
  ABSTRACT: Inherited white-matter disorders are a broad class of diseases for which treatment and classification are both challenging. Indeed, nearly half of the children presenting with a leukoencephalopathy remain without a specific diagnosis. Here, we report on the application of high-throughput genome and exome sequencing to a cohort of ten individuals with a leukoencephalopathy of unknown etiology and clinically characterized by hypomyelination with brain stem and spinal cord involvement and leg spasticity (HBSL), as well as the identification of compound-heterozygous and homozygous mutations in cytoplasmic aspartyl-tRNA synthetase (DARS). These mutations cause nonsynonymous changes to seven highly conserved amino acids, five of which are unchanged between yeast and man, in the DARS C-terminal lobe adjacent to, or within, the active-site pocket. Intriguingly, HBSL bears a striking resemblance to leukoencephalopathy with brain stem and spinal cord involvement and elevated lactate (LBSL), which is caused by mutations in the mitochondria-specific DARS2, suggesting that these two diseases might share a common underlying molecular pathology. These findings add to the growing body of evidence that mutations in tRNA synthetases can cause a broad range of neurologic disorders.
  The American Journal of Human Genetics 05/2013; 92(5):774-80.
• Article: Incidental variants are critical for genomics.

  Leslie G Biesecker
  [show abstract] [hide abstract]
  ABSTRACT: The topic of incidental variants detected through exome and genome sequencing is controversial, both in clinical practice and in research. The arguments for and against the deliberate analysis and return of incidental variants focus on issues of clinical validity, clinical utility, autonomy, clinical and research infrastructure and costs, and, in the research arena, therapeutic misconception. These topics are briefly reviewed and an argument is made that these variants are the future of genomic medicine. As a field, we should take full advantage of all opportunities to study these variants by searching them out, returning them to patients and research participants, and studying their utility for predictive medicine.
  The American Journal of Human Genetics 05/2013; 92(5):648-51.
• Article: MASTOR: Mixed-Model Association Mapping of Quantitative Traits in Samples with Related Individuals.

  Johanna Jakobsdottir, Mary Sara McPeek
  [show abstract] [hide abstract]
  ABSTRACT: Genetic association studies often sample individuals with known familial relationships in addition to unrelated individuals, and it is common for some individuals to have missing data (phenotypes, genotypes, or covariates). When some individuals in a sample are related, power can be gained by incorporating all individuals in the analysis, including individuals with partially missing data, while properly accounting for the dependence among them. We propose MASTOR, a mixed-model, retrospective score test for genetic association with a quantitative trait. MASTOR achieves high power in samples that contain related individuals by making full use of the relationship information to incorporate partially missing data in the analysis while correcting for dependence. Individuals with available phenotype and covariate information who are not genotyped but have genotyped relatives in the sample can still contribute to the association analysis because of the dependence among genotypes. Similarly, individuals who are genotyped but are missing covariate or phenotype information can contribute to the analysis. MASTOR is valid even when the phenotype model is misspecified and with either random or phenotype-based ascertainment. In simulations, we demonstrate the correct type 1 error of MASTOR, the increase in power that comes from making full use of the relationship information, the robustness to misspecification of the phenotype model, and the improvement in power that comes from modeling the heritability. We show that MASTOR is computationally feasible and practical in genome-wide association studies. We apply MASTOR to data on high-density lipoprotein cholesterol from the Framingham Heart study.
  The American Journal of Human Genetics 05/2013; 92(5):652-66.