Showing papers by "Stylianos E. Antonarakis published in 2016"

HGVS Recommendations for the Description of Sequence Variants: 2016 Update

Abstract: The consistent and unambiguous description of sequence variants is essential to report and exchange information on the analysis of a genome. In particular, DNA diagnostics critically depends on accurate and standardized description and sharing of the variants detected. The sequence variant nomenclature system proposed in 2000 by the Human Genome Variation Society has been widely adopted and has developed into an internationally accepted standard. The recommendations are currently commissioned through a Sequence Variant Description Working Group (SVD-WG) operating under the auspices of three international organizations: the Human Genome Variation Society (HGVS), the Human Variome Project (HVP), and the Human Genome Organization (HUGO). Requests for modifications and extensions go through the SVD-WG following a standard procedure including a community consultation step. Version numbers are assigned to the nomenclature system to allow users to specify the version used in their variant descriptions. Here, we present the current recommendations, HGVS version 15.11, and briefly summarize the changes that were made since the 2000 publication. Most focus has been on removing inconsistencies and tightening definitions allowing automatic data processing. An extensive version of the recommendations is available online, at http://www.HGVS.org/varnomen.

Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma

Abstract: Basal cell carcinoma (BCC) of the skin is the most common malignant neoplasm in humans. BCC is primarily driven by the Sonic Hedgehog (Hh) pathway. However, its phenotypic variation remains unexplained. Our genetic profiling of 293 BCCs found the highest mutation rate in cancer (65 mutations/Mb). Eighty-five percent of the BCCs harbored mutations in Hh pathway genes (PTCH1, 73% or SMO, 20% (P = 6.6 × 10(-8)) and SUFU, 8%) and in TP53 (61%). However, 85% of the BCCs also harbored additional driver mutations in other cancer-related genes. We observed recurrent mutations in MYCN (30%), PPP6C (15%), STK19 (10%), LATS1 (8%), ERBB2 (4%), PIK3CA (2%), and NRAS, KRAS or HRAS (2%), and loss-of-function and deleterious missense mutations were present in PTPN14 (23%), RB1 (8%) and FBXW7 (5%). Consistent with the mutational profiles, N-Myc and Hippo-YAP pathway target genes were upregulated. Functional analysis of the mutations in MYCN, PTPN14 and LATS1 suggested their potential relevance in BCC tumorigenesis.

APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication

Abstract: APOBEC3A and APOBEC3B, cytidine deaminases of the APOBEC family, are among the main factors causing mutations in human cancers. APOBEC deaminates cytosines in single-stranded DNA (ssDNA). A fraction of the APOBEC-induced mutations occur as clusters ("kataegis") in single-stranded DNA produced during repair of double-stranded breaks (DSBs). However, the properties of the remaining 87% of nonclustered APOBEC-induced mutations, the source and the genomic distribution of the ssDNA where they occur, are largely unknown. By analyzing genomic and exomic cancer databases, we show that >33% of dispersed APOBEC-induced mutations occur on the lagging strand during DNA replication, thus unraveling the major source of ssDNA targeted by APOBEC in cancer. Although methylated cytosine is generally more mutation-prone than nonmethylated cytosine, we report that methylation reduces the rate of APOBEC-induced mutations by a factor of roughly two. Finally, we show that in cancers with extensive APOBEC-induced mutagenesis, there is almost no increase in mutation rates in late replicating regions (contrary to other cancers). Because late-replicating regions are depleted in exons, this results in a 1.3-fold higher fraction of mutations residing within exons in such cancers. This study provides novel insight into the APOBEC-induced mutagenesis and describes the peculiarity of the mutational processes in cancers with the signature of APOBEC-induced mutations.

Pathogenic Variants in PIGG Cause Intellectual Disability with Seizures and Hypotonia.

Abstract: Glycosylphosphatidylinositol (GPI) is a glycolipid that anchors >150 various proteins to the cell surface. At least 27 genes are involved in biosynthesis and transport of GPI-anchored proteins (GPI-APs). To date, mutations in 13 of these genes are known to cause inherited GPI deficiencies (IGDs), and all are inherited as recessive traits. IGDs mainly manifest as intellectual disability, epilepsy, coarse facial features, and multiple organ anomalies. These symptoms are caused by the decreased surface expression of GPI-APs or by structural abnormalities of GPI. Here, we present five affected individuals (from two consanguineous families from Egypt and Pakistan and one non-consanguineous family from Japan) who show intellectual disability, hypotonia, and early-onset seizures. We identified pathogenic variants in PIGG, a gene in the GPI pathway. In the consanguineous families, homozygous variants c.928C>T (p.Gln310(∗)) and c.2261+1G>C were found, whereas the Japanese individual was compound heterozygous for c.2005C>T (p.Arg669Cys) and a 2.4 Mb deletion involving PIGG. PIGG is the enzyme that modifies the second mannose with ethanolamine phosphate, which is removed soon after GPI is attached to the protein. Physiological significance of this transient modification has been unclear. Using B lymphoblasts from affected individuals of the Egyptian and Japanese families, we revealed that PIGG activity was almost completely abolished; however, the GPI-APs had normal surface levels and normal structure, indicating that the pathogenesis of PIGG deficiency is not yet fully understood. The discovery of pathogenic variants in PIGG expands the spectrum of IGDs and further enhances our understanding of this etiopathogenic class of intellectual disability.

DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome

Abstract: Genomic imprinting is a mechanism in which gene expression varies depending on parental origin. Imprinting occurs through differential epigenetic marks on the two parental alleles, with most imprinted loci marked by the presence of differentially methylated regions (DMRs). To identify sites of parental epigenetic bias, here we have profiled DNA methylation patterns in a cohort of 57 individuals with uniparental disomy (UPD) for 19 different chromosomes, defining imprinted DMRs as sites where the maternal and paternal methylation levels diverge significantly from the biparental mean. Using this approach we identified 77 DMRs, including nearly all those described in previous studies, in addition to 34 DMRs not previously reported. These include a DMR at TUBGCP5 within the recurrent 15q11.2 microdeletion region, suggesting potential parent-of-origin effects associated with this genomic disorder. We also observed a modest parental bias in DNA methylation levels at every CpG analyzed across ∼1.9 Mb of the 15q11-q13 Prader-Willi/Angelman syndrome region, demonstrating that the influence of imprinting is not limited to individual regulatory elements such as CpG islands, but can extend across entire chromosomal domains. Using RNA-seq data, we detected signatures consistent with imprinted expression associated with nine novel DMRs. Finally, using a population sample of 4,004 blood methylomes, we define patterns of epigenetic variation at DMRs, identifying rare individuals with global gain or loss of methylation across multiple imprinted loci. Our data provide a detailed map of parental epigenetic bias in the human genome, providing insights into potential parent-of-origin effects.

Autosomal-Recessive Mutations in AP3B2, Adaptor-Related Protein Complex 3 Beta 2 Subunit, Cause an Early-Onset Epileptic Encephalopathy with Optic Atrophy

Abstract: Early-onset epileptic encephalopathy (EOEE) represents a heterogeneous group of severe disorders characterized by seizures, interictal epileptiform activity with a disorganized electroencephalography background, developmental regression or retardation, and onset before 1 year of age. Among a cohort of 57 individuals with epileptic encephalopathy, we ascertained two unrelated affected individuals with EOEE associated with developmental impairment and autosomal-recessive variants in AP3B2 by means of whole-exome sequencing. The targeted sequencing of AP3B2 in 86 unrelated individuals with EOEE led to the identification of an additional family. We gathered five additional families with eight affected individuals through the Matchmaker Exchange initiative by matching autosomal-recessive mutations in AP3B2. Reverse phenotyping of 12 affected individuals from eight families revealed a homogeneous EOEE phenotype characterized by severe developmental delay, poor visual contact with optic atrophy, and postnatal microcephaly. No spasticity, albinism, or hematological symptoms were reported. AP3B2 encodes the neuron-specific subunit of the AP-3 complex. Autosomal-recessive variations of AP3B1, the ubiquitous isoform, cause Hermansky-Pudlak syndrome type 2. The only isoform for the δ subunit of the AP-3 complex is encoded by AP3D1. Autosomal-recessive mutations in AP3D1 cause a severe disorder cumulating the symptoms of the AP3B1 and AP3B2 defects.

Experience of a multidisciplinary task force with exome sequencing for Mendelian disorders

Abstract: In order to optimally integrate the use of high-throughput sequencing (HTS) as a tool in clinical diagnostics of likely monogenic disorders, we have created a multidisciplinary “Genome Clinic Task Force” at the University Hospitals of Geneva, which is composed of clinical and molecular geneticists, bioinformaticians, technicians, bioethicists, and a coordinator. We have implemented whole exome sequencing (WES) with subsequent targeted bioinformatics analysis of gene lists for specific disorders. Clinical cases of heterogeneous Mendelian disorders that could potentially benefit from HTS are presented and discussed during the sessions of the task force. Debate concerning the interpretation of identified variants and the content of the final report constitutes a major part of the task force’s work. Furthermore, issues related to bioethics, genetic counseling, quality control, and reimbursement are also addressed. This multidisciplinary task force has enabled us to create a platform for regular exchanges between all involved experts in order to deal with the multiple complex issues related to HTS in clinical practice and to continuously improve the diagnostic use of HTS. In addition, this task force was instrumental to formally approve the reimbursement of HTS for molecular diagnosis of Mendelian disorders in Switzerland.

Exome sequencing discloses KALRN homozygous variant as likely cause of intellectual disability and short stature in a consanguineous pedigree.

Abstract: The recent availability of whole-exome sequencing has opened new possibilities for the evaluation of individuals with genetically undiagnosed intellectual disability. We report two affected siblings, offspring of first-cousin parents, with intellectual disability, hypotonia, short stature, growth hormone deficiency, and delayed bone age. All members of the nuclear family were genotyped, and exome sequencing was performed in one of the affected individuals. We used an in-house algorithm (CATCH v1.1) that combines homozygosity mapping with exome sequencing results and provides a list of candidate variants. One identified novel homozygous missense variant in KALRN (NM_003947.4:c.3644C>A: p.(Thr1215Lys)) was predicted to be pathogenic by all pathogenicity prediction software used (SIFT, PolyPhen, Mutation Taster). KALRN encodes the protein kalirin, which is a GTP-exchange factor protein with a reported role in cytoskeletal remodeling and dendritic spine formation in neurons. It is known that mice with ablation of Kalrn exhibit age-dependent functional deficits and behavioral phenotypes. Exome sequencing provided initial evidence linking KALRN to monogenic intellectual disability in man, and we propose that KALRN is the causative gene for the autosomal recessive phenotype in this family.

Pure Progressive Ataxia and Palatal Tremor (PAPT) Associated with a New Polymerase Gamma (POLG) Mutation.

Abstract: Progressive ataxia with palatal tremor (PAPT) is a syndrome caused by cerebellar and brainstem lesions involving the dentato-rubro-olivary tract and associated with hypertrophic olivary degeneration. Etiologies include acquired posterior fossa lesions (e.g. tumors, superficial siderosis, and inflammatory diseases) and genetic disorders, such as glial fibrillary acidic protein (GFAP) and polymerase gamma (POLG) mutations. We describe the case of a 52-year-old man who developed pure progressive ataxia and palatal tremor. Genetic analysis has shown that he is compound heterozygote for a known pathogenic (W748S) and a novel POLG variant (I1185N). Patients with POLG recessive mutations usually manifest a more complex clinical picture, including polyneuropathy and epilepsy; our case emphasizes the need to consider a genetic origin in a seemingly sporadic and pure PAPT.

Human genome meeting 2016: Houston, TX, USA. 28 February - 2 March 2016

Abstract: O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder

Corrigendum: Domains of genome-wide gene expression dysregulation in Down's syndrome.

Abstract: Nature 508, 345–350 (2014); doi:10.1038/nature13200 Owing to a labelling error in the input files, one of the two replicate data sets used for Fig. 5d and e and Supplementary Fig. 6d of this Article was incorrect. We have now repeated the analysis with a correct, independent replicate experiment. This confirms our previous conclusion that there are no detectable differences in nuclear lamina interactions between the normal and trisomy 21 twin cells.

Identification de nouveaux gènes impliqués dans les carcinomes basocellulaires sporadiques

Abstract: Introduction Les carcinomes basocellulaires (BCC) sont les cancers cutanes les plus frequents chez l’homme. Leur determinisme est lie a l’activation de la voie hedgehog, qui est actuellement la cible d’inhibiteurs specifiques. Neanmoins, l’implication de mutations dans des genes lies a d’autres voies physiopathologiques n’a pas ete exploree de facon systematique et exhaustive. Celles-ci pourraient intervenir dans l’agressivite tumorale et/ou la differentiation en sous-types histologiques particuliers. La recherche de variants de sequences dans l’ADN tumoral, a l’aide de techniques de sequencage a haut debit des parties codantes du genome (« exome sequencing »), est une premiere approche pour apprehender cette question. Materiel et methodes Materiel biologique : les echantillons tumoraux etaient obtenus soit en peroperatoire (punch), soit sur coupe histologique ; l’ADN controle etait obtenu sur sang peripherique. Au total, on disposait de 293 BCCs preleves sur 236 patients. Recherche de mutations : elle a ete realisee par sequencage d’exome dans un premier temps (n = 126), puis par sequencage d’un panel de 387 genes candidats (n = 167). Analyse d’expression : elle a ete realisee par RNA-sequencing comparatif entre tissu tumoral et peau saine sur 61 paires BCCs/peau adjacente. Resultats Le taux moyen de mutations pour les BCC etait de 65/Mb, soit le chiffre le plus eleve de tous les cancers humains. Ces mutations portaient la signature-UV dans 90 % des cas. Dans 85 % des BCCs, on trouvait des mutations affectant la voie hedgehog (PTCH, SMO, SUFU) et dans 63 % des mutations de P53. Cependant, 85 % des BCCs presentaient d’autres mutations sur des genes impliques dans d’autres cancers. Il s’agissait de mutations affectant MYCN (30 %), PPP6C (15 %), STK19 (10 %), LATS1 (8 %), ERBB2 (4 %), PIK3CA (2 %), ainsi que NRAS, KRAS et HRAS (2 %).D’autres mutations induisant une perte de fonction etaient presentes dans PTPN14 (23 %), RB1 (8 %) et FBXW7 (5 %). L’analyse d’expression des BCCs mutes pour MYCN et PTPN14 confirmait une surexpression des genes impliques dans ces 2 voies. De meme, les BCCs mutes pour les genes PTCH, SMO ou SUFU induisaient une activation de la voie hedgehog. Discussion Cette etude de sequencage a haut debit de 293 BCCs confirme l’implication des genes cles de la voie hedgehog. Surtout, comme cela a ete constate dans d’autres cancers ou hedgehog actives (e.g. medulloblastome), elle met en evidence des evenements moleculaires supplementaires, responsables de l’activation des voie MYCN ou YAP-Hippo. On entrevoit de surcroit une correlation avec certains sous-types histologiques plus agressifs. Conclusion L’ensemble de ces resultats offre de nouvelles cibles therapeutiques pour les BCCs complexes, inaccessibles au traitement chirurgical. C’est une premiere etape au decryptage moleculaire des evenements initiateurs du developpement tumoral ainsi que de la progression clinique des BCCs.

Origin of the /3-globin gene in Blacks mutation or gene conversion or both (haplotypes/hemoglobinopathies/sickle cell anemia/DNA polymorphis

Abstract: In order to investigate the origin(s) of the mutation(s) leading to the f.-globin gene in North American populations of African ancestry, we analyzed DNA polymor- phisms in the P-globin gene cluster in a large number of both pA_ and Ps-globin gene-bearing chromosomes in U.S. and Ja- maican Blacks. We found 16 different haplotypes of polymor- phic sites associated with 170 PS-globin gene-bearing chromo- somes. The three most common f3s haplotypes, which account for 151/170 of the 13s-globin gene-bearing chromosomes, are only rarely seen in the chromosomes bearing the lA-globin gene in these populations (6/47). Two observations suggest multiple origins or interallelic gene conversion, or both, of the fp mutation. First, the mutation is present in all three P-glo- bin gene frameworks. Second, the haplotypes can be divid- ed into four groups, each of which cannot be derived from any other by less than two crossing-over events. In summary, our observation of the f3 mutation on 16 different haplotypes in African populations can be best explained by (10 a number of simple recombination events 5' to the f-globin gene and (ii) up to four independent mutations and/or interallelic gene conver- sions.