De novo copy number variations in candidate genomic regions in patients of severe autism spectrum disorder in Vietnam.

Autism spectrum disorder (ASD) is a developmental disorder with a prevalence of around 1% children worldwide and characterized by patient behaviour (communication, social interaction, and personal development). Data on the efficacy of diagnostic tests using copy number variations (CNVs) in candidate genes in ASD is currently around 10% but it is overrepresented by patients of Caucasian background. We report here that the diagnostic success of de novo candidate CNVs in Vietnamese ASD patients is around 6%. We recruited one hundred trios (both parents and a child) where the child was clinically diagnosed with ASD while the parents were not affected. We performed genetic screening to exclude RETT syndrome and Fragile X syndrome and performed genome-wide DNA microarray (aCGH) on all probands and their parents to analyse for de novo CNVs. We detected 1708 non-redundant CNVs in 100 patients and 118 (7%) of them were de novo. Using the filter for known CNVs from the Simons Foundation Autism Research Initiative (SFARI) database, we identified six CNVs (one gain and five loss CNVs) in six patients (3 males and 3 females). Notably, 3 of our patients had a deletion involving the SHANK3 gene-which is the highest compared to previous reports. This is the first report of candidate CNVs in ASD patients from Vietnam and provides the framework for building a CNV based test as the first tier screening for clinical management.

Novel findings from family-based exome sequencing for children with biliary atresia.

Biliary atresia (BA) is a progressive inflammation and fibrosis of the biliary tree characterized by the obstruction of bile flow, which results in liver failure, scarring and cirrhosis. This study aimed to explore the elusive aetiology of BA by conducting whole exome sequencing for 41 children with BA and their parents (35 trios, including 1 family with 2 BA-diagnosed children and 5 child-mother cases). We exclusively identified and validated a total of 28 variants (17 X-linked, 6 de novo and 5 homozygous) in 25 candidate genes from our BA cohort. These variants were among the 10% most deleterious and had a low minor allele frequency against the employed databases: Kinh Vietnamese (KHV), GnomAD and 1000 Genome Project. Interestingly, AMER1, INVS and OCRL variants were found in unrelated probands and were first reported in a BA cohort. Liver specimens and blood samples showed identical variants, suggesting that somatic variants were unlikely to occur during morphogenesis. Consistent with earlier attempts, this study implicated genetic heterogeneity and non-Mendelian inheritance of BA.

Genetic landscape of autism spectrum disorder in Vietnamese children.

Autism spectrum disorder (ASD) is a complex disorder with an unclear aetiology and an estimated global prevalence of 1%. However, studies of ASD in the Vietnamese population are limited. Here, we first conducted whole exome sequencing (WES) of 100 children with ASD and their unaffected parents. Our stringent analysis pipeline was able to detect 18 unique variants (8 de novo and 10 ×-linked, all validated), including 12 newly discovered variants. Interestingly, a notable number of X-linked variants were detected (56%), and all of them were found in affected males but not in affected females. We uncovered 17 genes from our ASD cohort in which CHD8, DYRK1A, GRIN2B, SCN2A, OFD1 and MDB5 have been previously identified as ASD risk genes, suggesting the universal aetiology of ASD for these genes. In addition, we identified six genes that have not been previously reported in any autism database: CHM, ENPP1, IGF1, LAS1L, SYP and TBX22. Gene ontology and phenotype-genotype analysis suggested that variants in IGF1, SYP and LAS1L could plausibly confer risk for ASD. Taken together, this study adds to the genetic heterogeneity of ASD and is the first report elucidating the genetic landscape of ASD in Vietnamese children.

A novel de novo variant of LAMA2 contributes to merosin deficient congenital muscular dystrophy type 1A: Case report.

Merosin deficient congenital muscular dystrophy type 1A (MDC1A) is caused by defects in the LAMA2 gene. Patients with MDC1A exhibit severe symptoms, including congenital hypotonia, delayed motor development and contractures. The present case report describes a Vietnamese male child with clinical manifestations of delayed motor development, limb-girdle muscular dystrophy, severe scoliosis and white matter abnormality in the brain. Whole exome sequencing (WES) was performed with subsequent validation using Sanger sequencing, and a de novo missense variant (NM_000426.3:c.1964T>C, p.Leu655Pro) and a splice site variant (NG_008678.1:c.3556-13T>A) in the LAMA2 gene of the proband was detected. The missense variant located in exon 14 and has not been reported previously, to the best of our knowledge; whereas the splice site variant has been previously reported to cause premature termination of transcription in patients with MDC1A. In silico tools predicted that the missense variant was damaging. Phenotype-genotype analysis suggested that this proband was associated with classical early onset MDC1A. The co-existence of a de novo and a heterozygous variant in the LAMA2 gene suggested that the de novo variant contributed to the autosomal recessive manner of the disease. Careful consideration of this event by clinical confirmation of parental carrier status may help to accurately determine the risk of occurrence of this disease in future offspring. Additionally, WES is recommended as a powerful tool to assist in identifying potentially causative variants for heterogeneous diseases such as MDC1A.

Improved mitochondrial amino acid substitution models for metazoan evolutionary studies.

BACKGROUND: Amino acid substitution models play an essential role in inferring phylogenies from mitochondrial protein data. However, only few empirical models have been estimated from restricted mitochondrial protein data of a hundred species. The existing models are unlikely to represent appropriately the amino acid substitutions from hundred thousands metazoan mitochondrial protein sequences. RESULTS: We selected 125,935 mitochondrial protein sequences from 34,448 species in the metazoan kingdom to estimate new amino acid substitution models targeting metazoa, vertebrates and invertebrate groups. The new models help to find significantly better likelihood phylogenies in comparison with the existing models. We noted remarkable distances from phylogenies with the existing models to the maximum likelihood phylogenies that indicate a considerable number of incorrect bipartitions in phylogenies with the existing models. Finally, we used the new models and mitochondrial protein data to certify that Testudines, Aves, and Crocodylia form one separated clade within amniotes. CONCLUSIONS: We introduced new mitochondrial amino acid substitution models for metazoan mitochondrial proteins. The new models outperform the existing models in inferring phylogenies from metazoan mitochondrial protein data. We strongly recommend researchers to use the new models in analysing metazoan mitochondrial protein data.

Building Ancestral Recombination Graphs for Whole Genomes.

We propose a heuristic algorithm, called ARG4WG, to build plausible ancestral recombination graphs (ARGs) from thousands of whole genome samples. By using the longest shared end for recombination inference, ARG4WG constructs ARGs with small numbers of recombination events that perform well in association mapping on genome-wide association studies.

Mechanisms of sex determination and transmission ratio distortion in Aedes aegypti.

BACKGROUND: More effective mosquito control strategies are urgently required due to the increasing prevalence of insecticide resistance. The sterile insect technique (SIT) and the release of insects carrying a dominant lethal allele (RIDL) are two proposed methods for environmentally-friendly, species-targeted population control. These methods may be more suitable for developing countries if producers reduce the cost of rearing insects. The cost of control programs could be reduced by producing all-male mosquito populations to circumvent the isolation of females before release without reducing male mating competitiveness caused by transgenes. RESULTS: An RNAi construct targeting the RNA recognition motif of the Aedes aegypti transformer-2 (tra-2) gene does not trigger female-to-male sex conversion as commonly observed among dipterous insects. Instead, homozygous insects show greater mortality among m-chromosome-bearing sperm and mm zygotes, yielding up to 100% males in the subsequent generations. The performance of transgenic males was not significantly different to wild-type males in narrow-cage competitive mating experiments. CONCLUSION: Our data provide preliminary evidence that the knockdown of Ae. aegypti tra-2 gene expression causes segregation distortion acting at the level of gametic function, which is reinforced by sex-specific zygotic lethality. This finding could promote the development of new synthetic sex distorter systems for the production of genetic sexing mosquito strains.

FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets.

BACKGROUND: Amino acid replacement rate matrices are a crucial component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Ideally, the rate matrix reflects the mutational behavior of the actual data under study; however, estimating amino acid replacement rate matrices requires large protein alignments and is computationally expensive and complex. As a compromise, sub-optimal pre-calculated generic matrices are typically used for protein-based phylogeny. Sequence availability has now grown to a point where problem-specific rate matrices can often be calculated if the computational cost can be controlled. RESULTS: The most time consuming step in estimating rate matrices by maximum likelihood is building maximum likelihood phylogenetic trees from protein alignments. We propose a new procedure, called FastMG, to overcome this obstacle. The key innovation is the alignment-splitting algorithm that splits alignments with many sequences into non-overlapping sub-alignments prior to estimating amino acid replacement rates. Experiments with different large data sets showed that the FastMG procedure was an order of magnitude faster than without splitting. Importantly, there was no apparent loss in matrix quality if an appropriate splitting procedure is used. CONCLUSIONS: FastMG is a simple, fast and accurate procedure to estimate amino acid replacement rate matrices from large data sets. It enables researchers to study the evolutionary relationships for specific groups of proteins or taxa with optimized, data-specific amino acid replacement rate matrices. The programs, data sets, and the new mammalian mitochondrial protein rate matrix are available at http://fastmg.codeplex.com.

ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.

SUMMARY: Amino acid replacement rate matrices are an essential basis of protein studies (e.g. in phylogenetics and alignment). A number of general purpose matrices have been proposed (e.g. JTT, WAG, LG) since the seminal work of Margaret Dayhoff and co-workers. However, it has been shown that matrices specific to certain protein groups (e.g. mitochondrial) or life domains (e.g. viruses) differ significantly from general average matrices, and thus perform better when applied to the data to which they are dedicated. This Web server implements the maximum-likelihood estimation procedure that was used to estimate LG, and provides a number of tools and facilities. Users upload a set of multiple protein alignments from their domain of interest and receive the resulting matrix by email, along with statistics and comparisons with other matrices. A non-parametric bootstrap is performed optionally to assess the variability of replacement rate estimates. Maximum-likelihood trees, inferred using the estimated rate matrix, are also computed optionally for each input alignment. Finely tuned procedures and up-to-date ML software (PhyML 3.0, XRATE) are combined to perform all these heavy calculations on our clusters. AVAILABILITY: http://www.atgc-montpellier.fr/ReplacementMatrix/ CONTACT: olivier.gascuel@lirmm.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at http://www.atgc-montpellier.fr/ReplacementMatrix/

FLU, an amino acid substitution model for influenza proteins.

BACKGROUND: The amino acid substitution model is the core component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Although several general amino acid substitution models have been estimated from large and diverse protein databases, they remain inappropriate for analyzing specific species, e.g., viruses. Emerging epidemics of influenza viruses raise the need for comprehensive studies of these dangerous viruses. We propose an influenza-specific amino acid substitution model to enhance the understanding of the evolution of influenza viruses. RESULTS: A maximum likelihood approach was applied to estimate an amino acid substitution model (FLU) from approximately 113,000 influenza protein sequences, consisting of approximately 20 million residues. FLU outperforms 14 widely used models in constructing maximum likelihood phylogenetic trees for the majority of influenza protein alignments. On average, FLU gains approximately 42 log likelihood points with an alignment of 300 sites. Moreover, topologies of trees constructed using FLU and other models are frequently different. FLU does indeed have an impact on likelihood improvement as well as tree topologies. It was implemented in PhyML and can be downloaded from ftp://ftp.sanger.ac.uk/pub/1000genomes/lsq/FLU or included in PhyML 3.0 server at http://www.atgc-montpellier.fr/phyml/. CONCLUSIONS: FLU should be useful for any influenza protein analysis system which requires an accurate description of amino acid substitutions.