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Molecular Genetics & Genomic Medicine Volume 2 Issue 5 is Published!

September 10, 2014

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 ε4 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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