Molecular Genetics & Genomic Medicine has now published its next issue. Editor-in-Chief: Max Muenke introduces his editorial highlights: “This issue includes an Invited Commentary on the evolution of comparative genomics and also features the next article in our series, “Genetics and Genomic Medicine around the World“, this month focusing on Saudi Arabia. Highlights of the issue include articles focusing on craniofacial morphometric analysis in X-linked hypohidrotic ectodermal dysplasia, coding region analysis in centenarians, next generation sequencing for Usher syndrome and polycystic kidney disease.”

Craniofacial morphometric analysis of individuals with X-linked hypohidrotic ectodermal dysplasia by Alice F. Goodwin, Jacinda R. Larson, Kyle B. Jones, Denise K. Liberton, Maya Landan, Zhifeng Wang, Anne Boekelheide, Margaret Langham, Vagan Mushegyan, Snehlata Oberoi, Rosalie Brao, Timothy Wen, Ramsey Johnson, Kenneth Huttner, Dorothy K. Grange, Richard A. Spritz, Benedikt Hallgrímsson, Andrew H. Jheon and Ophir D. Klein.
Abstract: Hypohidrotic ectodermal dysplasia (HED) is the most prevalent type of ectodermal dysplasia (ED). ED is an umbrella term for a group of syndromes characterized by missing or malformed ectodermal structures, including skin, hair, sweat glands, and teeth. The X-linked recessive (XL), autosomal recessive (AR), and autosomal dominant (AD) types of HED are caused by mutations in the genes encoding ectodysplasin (EDA1), EDA receptor (EDAR), or EDAR-associated death domain (EDARADD). Patients with HED have a distinctive facial appearance, yet a quantitative analysis of the HED craniofacial phenotype using advanced three-dimensional (3D) technologies has not been reported. In this study, we characterized craniofacial morphology in subjects with X-linked hypohidrotic ectodermal dysplasia (XLHED) by use of 3D imaging and geometric morphometrics (GM), a technique that uses defined landmarks to quantify size and shape in complex craniofacial morphologies. We found that the XLHED craniofacial phenotype differed significantly from controls. Patients had a smaller and shorter face with a proportionally longer chin and midface, prominent midfacial hypoplasia, a more protrusive chin and mandible, a narrower and more pointed nose, shorter philtrum, a narrower mouth, and a fuller and more rounded lower lip. Our findings refine the phenotype of XLHED and may be useful both for clinical diagnosis of XLHED and to extend understanding of the role of EDA in craniofacial development.

Disease variants in genomes of 44 centenarians by Yun Freudenberg-Hua, Jan Freudenberg, Vladimir Vacic, Avinash Abhyankar, Anne-Katrin Emde, Danny Ben-Avraham, Nir Barzilai, Dayna Oschwald, Erika Christen, Jeremy Koppel, Blaine Greenwald, Robert B. Darnell, Soren Germer, Gil Atzmon and Peter Davies.
Abstract: To identify previously reported disease mutations that are compatible with extraordinary longevity, we screened the coding regions of the genomes of 44 Ashkenazi Jewish centenarians. Individual genome sequences were generated with 30× coverage on the Illumina HiSeq 2000 and single-nucleotide variants were called with the genome analysis toolkit (GATK). We identified 130 coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database and that are infrequent in the general population. These variants were previously reported to cause a wide range of degenerative, neoplastic, and cardiac diseases with autosomal dominant, autosomal recessive, and X-linked inheritance. Several of these variants are located in genes that harbor actionable incidental findings, according to the recommendations of the American College of Medical Genetics. In addition, we found risk variants for late-onset neurodegenerative diseases, such as the APOE ?4 allele that was even present in a homozygous state in one centenarian who did not develop Alzheimer’s disease. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions.

Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome by Peter M. Krawitz, Daniela Schiska, Ulrike Krüger, Sandra Appelt, Verena Heinrich, Dmitri Parkhomchuk, Bernd Timmermann, Jose M. Millan, Peter N. Robinson, Stefan Mundlos, Jochen Hecht and Manfred Gross.
Abstract: Usher syndrome is an autosomal recessive disorder characterized both by deafness and blindness. For the three clinical subtypes of Usher syndrome causal mutations in altogether 12 genes and a modifier gene have been identified. Due to the genetic heterogeneity of Usher syndrome, the molecular analysis is predestined for a comprehensive and parallelized analysis of all known genes by next-generation sequencing (NGS) approaches. We describe here the targeted enrichment and deep sequencing for exons of Usher genes and compare the costs and workload of this approach compared to Sanger sequencing. We also present a bioinformatics analysis pipeline that allows us to detect single-nucleotide variants, short insertions and deletions, as well as copy number variations of one or more exons on the same sequence data. Additionally, we present a flexible in silico gene panel for the analysis of sequence variants, in which newly identified genes can easily be included. We applied this approach to a cohort of 44 Usher patients and detected biallelic pathogenic mutations in 35 individuals and monoallelic mutations in eight individuals of our cohort. Thirty-nine of the sequence variants, including two heterozygous deletions comprising several exons of USH2A, have not been reported so far. Our NGS-based approach allowed us to assess single-nucleotide variants, small indels, and whole exon deletions in a single test. The described diagnostic approach is fast and cost-effective with a high molecular diagnostic yield.

Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing by Daniel Trujillano, Gemma Bullich, Stephan Ossowski, José Ballarín, Roser Torra, Xavier Estivill and Elisabet Ars.
Abstract: Molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) relies on mutation screening of PKD1 and PKD2, which is complicated by extensive allelic heterogeneity and the presence of six highly homologous sequences of PKD1. To date, specific sequencing of PKD1 requires laborious long-range amplifications. The high cost and long turnaround time of PKD1 and PKD2 mutation analysis using conventional techniques limits its widespread application in clinical settings. We performed targeted next-generation sequencing (NGS) of PKD1 and PKD2. Pooled barcoded DNA patient libraries were enriched by in-solution hybridization with PKD1 and PKD2 capture probes. Bioinformatics analysis was performed using an in-house developed pipeline. We validated the assay in a cohort of 36 patients with previously known PKD1 and PKD2 mutations and five control individuals. Then, we used the same assay and bioinformatics analysis in a discovery cohort of 12 uncharacterized patients. We detected 35 out of 36 known definitely, highly likely, and likely pathogenic mutations in the validation cohort, including two large deletions. In the discovery cohort, we detected 11 different pathogenic mutations in 10 out of 12 patients. This study demonstrates that laborious long-range PCRs of the repeated PKD1 region can be avoided by in-solution enrichment of PKD1 and PKD2 and NGS. This strategy significantly reduces the cost and time for simultaneous PKD1 and PKD2 sequence analysis, facilitating routine genetic diagnostics of ADPKD.

The journal also publishes Genetics and Genomic Medicine around the World. Below is the second article of this type, this month focusing on Saudi Arabia.

“Genetics and genomic medicine in Saudi Arabia” by Fowzan S. Alkuraya.

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Molecular Genetics & Genomic Medicine has now published its next issue. Editor-in-Chief: Max Muenke introduces his editorial highlights: “This issue includes an Invited Commentary on the genomics and epigenomics of substance use disorders and also features the third article in our series, “Genetics and Genomic Medicine around the World”, this month focusing on Brazil. Highlights of the issue include the articles, “Telomere Length, Family History and Paternal Age in Schizophrenia“, “Association of the c.385C>A (p.Pro129Thr) Polymorphism of the Fatty Acid Amide Hydrolase Gene with Anorexia Nervosa in the Japanese Population”, and “46,XY Disorder of Sexual Development Resulting from a Novel Monoallelic Mutation (p.Ser31Phe) in the Steroid 5?-Reductase Type-2 (SRD5A2) Gene”.

Telomere length, family history, and paternal age in schizophrenia by Dolores Malaspina, Roberta Dracxler, Julie Walsh-Messinger, Susan Harlap, Raymond R. Goetz, David Keefe and Mary C. Perrin.
Abstract: Leukocyte telomere length (LTL) is longer in association with advanced paternal age, but this association has not been examined along with family history (FH) in schizophrenia. LTL was measured by PCR and compared across cases and controls as part of a study to examine the characteristics of paternal age related schizophrenia. The 53 schizophrenia cases had similar mean LTL as 20 controls, although cases were significantly older than controls and overwhelmingly smoked cigarettes. Multivariate analyses showed that a FH of schizophrenia was associated with longer LTL in both male and female cases. Later paternal age was also related to longer LTL in male cases, but with shorter LTL in female cases. Male cases with older fathers and a FH had the longest LTL. The genetic architecture associated with a familial risk for schizophrenia may include pathways that lengthen LTL. Paternal aging conferred an additional increase in LTL lengthening in male cases, but reduced LTL in female cases. The gender difference in LTL for paternal aging is consistent with the severe illness features reported for female cases with older fathers and could implicate epigenetic alterations in the paternal X chromosomal region with advanced paternal age in association with the risk for schizophrenia.

Association of the c.385C>A (p.Pro129Thr) Polymorphism of the Fatty Acid Amide Hydrolase Gene with Anorexia Nervosa in the Japanese Population by Tetsuya Ando, Naho Tamura, Takashi Mera, Chihiro Morita, Michiko Takei, Chiemi Nakamoto, Masanori Koide, Mari Hotta, Tetsuro Naruo, Keisuke Kawai, Toshihiro Nakahara, Chikara Yamaguchi, Toshihiko Nagata, Kazuyoshi Ookuma, Yuri Okamoto, Takao Yamanaka, Nobuo Kiriike, Yuhei Ichimaru, Toshio Ishikawa, Gen Komaki and The Japanese Genetic Research Group For Eating Disorders.
Abstract: The functional c.385C>A single-nucleotide polymorphism (SNP) in the fatty acid amide hydrolase (FAAH) gene, one of the major degrading enzymes of endocannabinoids, is reportedly associated with anorexia nervosa (AN). We genotyped the c.385C>A SNP (rs324420) in 762 lifetime AN and 605 control participants in Japan. There were significant differences in the genotype and allele frequencies of c.385C>A between the AN and control groups. The minor 385A allele was less frequent in the AN participants than in the controls (allele-wise, odds ratio = 0.799, 95% confidence interval [CI] 0.653–0.976, P = 0.028). When the cases were subdivided into lifetime restricting subtype AN and AN with a history of binge eating or purging, only the restricting AN group exhibited a significant association (allele-wise, odds ratio = 0.717, 95% CI 0.557–0.922, P = 0.0094). Our results suggest that having the minor 385A allele of the FAAH gene may be protective against AN, especially restricting AN. This finding supports the possible role of the endocannabinoid system in susceptibility to AN.

46,XY Disorder of Sexual Development Resulting from a Novel Monoallelic Mutation (p.Ser31Phe) in the Steroid 5?-Reductase Type-2 (SRD5A2) Gene by Bertha Chávez, Luis Ramos, Rita Gómez and Felipe Vilchis.
Abstract: Inactivating mutations of the 5?-steroid reductase type-2 (SRD5A2) gene result in a broad spectrum of masculinization defects, ranging from a male phenotype with hypospadias to a female phenotype with Wolffian structures. Molecular studies of the SRD5A2 revealed a new heterozygous gene variant within the coding region that results in phenotypic expression. A c.92C>T transition changing serine to phenylalanine at codon 31 of exon 1 (p.Ser31Phe) was identified in a patient with 46,XY disorder of sexual development who displayed glandular hypospadias with micropenis and bilateral cryptorchidism. The restoration of the p.Ser31Phe mutation by site-directed mutagenesis and transient expression assays using cultured HEK-293 cells showed that this novel substitution does not abolish but does deregulate the catalytic efficiency of the enzyme. Thus, the maximum velocity (Vmax) value was higher for the mutant enzyme (22.5 ± 6.9 nmol DHT mg protein?1 h?1) than for the wild-type enzyme (9.8 ± 2.0 nmol DHT mg protein?1 h?1). Increased in vitro activity of the p.Ser31Phe mutant suggested an activating effect. This case provides evidence that heterozygous missense mutations in SRD5A2 may induce the abnormal development of male external genitalia..

The journal also publishes Genetics and Genomic Medicine around the World. Below is the second article of this type, this month focusing on Brazil.

“Genetics and genomics in Brazil: a promising future” by Maria Rita Passos-Bueno, Debora Bertola, Dafne Dain Gandelman Horovitz, Victor Evangelista de Faria Ferraz and Luciano Abreu Brito.

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Molecular Genetics & Genomic Medicine has now published its next issue. Editor-in-Chief: Max Muenke introduces his editorial highlights: “This issue includes an Invited Commentary on the Future of Genomic Medicine, HLA haplotyping, Papillon-Lefèvre syndrome, and association of THAP1 mutations with Primary Dystonia. It also features the second article in our series Genetics and Genomic Medicine around the World, this month focusing on Thailand. Highlights of the issue include the articles, “Novel IRF6 Mutations in Families with Van Der Woude Syndrome and Popliteal Pterygium Syndrome from Sub-Saharan Africa”, and “Mutations of NOTCH3 in childhood pulmonary arterial hypertension”.

Novel IRF6 Mutations in Families with Van Der Woude Syndrome and Popliteal Pterygium Syndrome from Sub-Saharan Africa by Azeez Butali, Peter A. Mossey, Wasiu L. Adeyemo, Mekonen A. Eshete, LauRen A. Gaines, Dee Even, Ramat O. Braimah, Babatunde S. Aregbesola, Jennifer V. Rigdon, Christian I. Emeka, Olutayo James, Mobolanle O. Ogunlewe, Akinola L. Ladeinde, Fikre Abate, Taye Hailu, Ibrahim Mohammed, Paul E. Gravem, Milliard Deribew, Mulualem Gesses, Adebowale A. Adeyemo and Jeffrey C. Murray.
Abstract: Orofacial clefts (OFC) are complex genetic traits that are often classified as syndromic or nonsyndromic clefts. Currently, there are over 500 types of syndromic clefts in the Online Mendelian Inheritance in Man (OMIM) database, of which Van der Woude syndrome (VWS) is one of the most common (accounting for 2% of all OFC). Popliteal pterygium syndrome (PPS) is considered to be a more severe form of VWS. Mutations in the IRF6 gene have been reported worldwide to cause VWS and PPS. Here, we report studies of families with VWS and PPS in sub-Saharan Africa. We screened the DNA of eight families with VWS and one family with PPS from Nigeria and Ethiopia by Sanger sequencing of the most commonly affected exons in IRF6 (exons 3, 4, 7, and 9). For the VWS families, we found a novel nonsense variant in exon 4 (p.Lys66X), a novel splice-site variant in exon 4 (p.Pro126Pro), a novel missense variant in exon 4 (p.Phe230Leu), a previously reported splice-site variant in exon 7 that changes the acceptor splice site, and a known missense variant in exon 7 (p.Leu251Pro). A previously known missense variant was found in exon 4 (p.Arg84His) in the PPS family. All the mutations segregate in the families. Our data confirm the presence of IRF6-related VWS and PPS in sub-Saharan Africa and highlights the importance of screening for novel mutations in known genes when studying diverse global populations. This is important for counseling and prenatal diagnosis for high-risk families.

Mutations of NOTCH3 in childhood pulmonary arterial hypertension by Ayako Chida, Masaki Shintani, Yoshihisa Matsushita, Hiroki Sato, Takahiro Eitoku, Tomotaka Nakayama, Yoshiyuki Furutani, Emiko Hayama, Yoichi Kawamura, Kei Inai, Shinichi Ohtsuki, Tsutomu Saji, Shigeaki Nonoyama and Toshio Nakanishi.
Abstract: Mutations of BMPR2 and other TGF-? superfamily genes have been reported in pulmonary arterial hypertension (PAH). However, 60–90% of idiopathic PAH cases have no mutations in these genes. Recently, the expression of NOTCH3 was shown to be increased in the pulmonary artery smooth muscle cells of PAH patients. We sought to investigate NOTCH3 and its target genes in PAH patients and clarify the role of NOTCH3 signaling. We screened for mutations in NOTCH3, HES1, and HES5 in 41 PAH patients who had no mutations in BMPR2, ALK1, endoglin, SMAD1/4/8, BMPR1B, or Caveolin-1. Two novel missense mutations (c.2519 G>A p.G840E, c.2698 A>C p.T900P) in NOTCH3 were identified in two PAH patients. We performed functional analysis using stable cell lines expressing either wild-type or mutant NOTCH3. The protein-folding chaperone GRP78/BiP was colocalized with wild-type NOTCH3 in the endoplasmic reticulum, whereas the majority of GRP78/BiP was translocated into the nuclei of cells expressing mutant NOTCH3. Cell proliferation and viability were higher for cells expressing mutant NOTCH3 than for those expressing wild-type NOTCH3. We identified novel NOTCH3 mutations in PAH patients and revealed that these mutations were involved in cell proliferation and viability. NOTCH3 mutants induced an impairment in NOTCH3-HES5 signaling. The results may contribute to the elucidation of PAH pathogenesis.

The journal also publishes Genetics and Genomic Medicine around the World. Below is the second article of this type, this month focusing on Thailand.

“Genetics and genomics in Thailand: challenges and opportunities” by Vorasuk Shotelersuk, Chanin Limwongse and Surakameth Mahasirimongkol

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Molecular Genetics & Genomic Medicine has now published its next issue. Editor-in-Chief: Max Muenke introduces his editorial highlights: “This issue includes an Invited Commentary on the Future of Genomic Medicine, HLA haplotyping, Papillon-Lefèvre syndrome, and association of THAP1 mutations with Primary Dystonia. It also features the second article in our series Genetics and Genomic Medicine around the World, this month focusing on Thailand. Highlights of the issue include the articles, “Novel IRF6 Mutations in Families with Van Der Woude Syndrome and Popliteal Pterygium Syndrome from Sub-Saharan Africa”, and “Mutations of NOTCH3 in childhood pulmonary arterial hypertension”.

Novel IRF6 Mutations in Families with Van Der Woude Syndrome and Popliteal Pterygium Syndrome from Sub-Saharan Africa by Azeez Butali, Peter A. Mossey, Wasiu L. Adeyemo, Mekonen A. Eshete, LauRen A. Gaines, Dee Even, Ramat O. Braimah, Babatunde S. Aregbesola, Jennifer V. Rigdon, Christian I. Emeka, Olutayo James, Mobolanle O. Ogunlewe, Akinola L. Ladeinde, Fikre Abate, Taye Hailu, Ibrahim Mohammed, Paul E. Gravem, Milliard Deribew, Mulualem Gesses, Adebowale A. Adeyemo and Jeffrey C. Murray.
Abstract: Orofacial clefts (OFC) are complex genetic traits that are often classified as syndromic or nonsyndromic clefts. Currently, there are over 500 types of syndromic clefts in the Online Mendelian Inheritance in Man (OMIM) database, of which Van der Woude syndrome (VWS) is one of the most common (accounting for 2% of all OFC). Popliteal pterygium syndrome (PPS) is considered to be a more severe form of VWS. Mutations in the IRF6 gene have been reported worldwide to cause VWS and PPS. Here, we report studies of families with VWS and PPS in sub-Saharan Africa. We screened the DNA of eight families with VWS and one family with PPS from Nigeria and Ethiopia by Sanger sequencing of the most commonly affected exons in IRF6 (exons 3, 4, 7, and 9). For the VWS families, we found a novel nonsense variant in exon 4 (p.Lys66X), a novel splice-site variant in exon 4 (p.Pro126Pro), a novel missense variant in exon 4 (p.Phe230Leu), a previously reported splice-site variant in exon 7 that changes the acceptor splice site, and a known missense variant in exon 7 (p.Leu251Pro). A previously known missense variant was found in exon 4 (p.Arg84His) in the PPS family. All the mutations segregate in the families. Our data confirm the presence of IRF6-related VWS and PPS in sub-Saharan Africa and highlights the importance of screening for novel mutations in known genes when studying diverse global populations. This is important for counseling and prenatal diagnosis for high-risk families.

Mutations of NOTCH3 in childhood pulmonary arterial hypertension by Ayako Chida, Masaki Shintani, Yoshihisa Matsushita, Hiroki Sato, Takahiro Eitoku, Tomotaka Nakayama, Yoshiyuki Furutani, Emiko Hayama, Yoichi Kawamura, Kei Inai, Shinichi Ohtsuki, Tsutomu Saji, Shigeaki Nonoyama and Toshio Nakanishi.
Abstract: Mutations of BMPR2 and other TGF-? superfamily genes have been reported in pulmonary arterial hypertension (PAH). However, 60–90% of idiopathic PAH cases have no mutations in these genes. Recently, the expression of NOTCH3 was shown to be increased in the pulmonary artery smooth muscle cells of PAH patients. We sought to investigate NOTCH3 and its target genes in PAH patients and clarify the role of NOTCH3 signaling. We screened for mutations in NOTCH3, HES1, and HES5 in 41 PAH patients who had no mutations in BMPR2, ALK1, endoglin, SMAD1/4/8, BMPR1B, or Caveolin-1. Two novel missense mutations (c.2519 G>A p.G840E, c.2698 A>C p.T900P) in NOTCH3 were identified in two PAH patients. We performed functional analysis using stable cell lines expressing either wild-type or mutant NOTCH3. The protein-folding chaperone GRP78/BiP was colocalized with wild-type NOTCH3 in the endoplasmic reticulum, whereas the majority of GRP78/BiP was translocated into the nuclei of cells expressing mutant NOTCH3. Cell proliferation and viability were higher for cells expressing mutant NOTCH3 than for those expressing wild-type NOTCH3. We identified novel NOTCH3 mutations in PAH patients and revealed that these mutations were involved in cell proliferation and viability. NOTCH3 mutants induced an impairment in NOTCH3-HES5 signaling. The results may contribute to the elucidation of PAH pathogenesis.

The journal also publishes Genetics and Genomic Medicine around the World. Below is the second article of this type, this month focusing on Thailand.

“Genetics and genomics in Thailand: challenges and opportunities” by Vorasuk Shotelersuk, Chanin Limwongse and Surakameth Mahasirimongkol

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Submit your article here.