PubMed | Shenzhen University, Copenhagen University, BGI Shenzhen, South China University of Technology and 4 more.
Type: | Journal: Scientific reports | Year: 2016
Y-chromosomal microdeletion (YCM) serves as an important genetic factor in non-obstructive azoospermia (NOA). Multiplex polymerase chain reaction (PCR) is routinely used to detect YCMs by tracing sequence-tagged sites (STSs) in the Y chromosome. Here we introduce a novel methodology in which we sequence 1,787 (post-filtering) STSs distributed across the entire male-specific Y chromosome (MSY) in parallel to uncover known and novel YCMs. We validated this approach with 766 Chinese men with NOA and 683 ethnically matched healthy individuals and detected 481 and 98 STSs that were deleted in the NOA and control group, representing a substantial portion of novel YCMs which significantly influenced the functions of spermatogenic genes. The NOA patients tended to carry more and rarer deletions that were enriched in nearby intragenic regions. Haplogroup O2* was revealed to be a protective lineage for NOA, in which the enrichment of b1/b3 deletion in haplogroup C was also observed. In summary, our work provides a new high-resolution portrait of deletions in the Y chromosome.
Sun Y.,BGI Shenzhen |
Wang L.,Huazhong University of Science and Technology |
Wei X.,BGI Shenzhen |
Zhu Q.,BGI Shenzhen |
And 9 more authors.
Clinica Chimica Acta | Year: 2013
Background: Autosomal recessive Zellweger spectrum disorder (ZSD), the main subgroup of the peroxisome biogenesis disorders (PBDs), can be caused by mutations in any of the 13 PEX genes. Zellweger syndrome (ZS) is the most common and severe phenotype in the heterogeneous ZSD. For the large number genes involved, it is difficult to make a precise genetic diagnosis by traditional methods at a time. A combination of enrichment of targeted genes and next-generation sequencing (NGS) would result in both high efficiency and low cost for targeted sequencing of genes of interest. Methods: To identify potential mutations in a Chinese family associated with Zellweger syndrome, 1930. kb of all the targeted region of PEX genes were captured and sequenced using NGS. We also performed Sanger sequencing to validate the NGS results. Results: Here, we reported a Chinese patient diagnosed as a severe classic type of PBD based on a clinical investigation. We then performed microarray-based NGS to detect the variants in PEX genes of the whole family. One reported heterozygosis mutation (c.782_783delAA) was identified in the patient's father and one novel heterozygosis missense mutation (c.475G. >. C) was found in the patient's mother, the patient inherited both mutations. Conclusions: The results proved that the application of target sequence capture using chip and high-throughput NGS is a valuable tool for the molecular diagnosis of peroxisome biogenesis disorders. The accuracy, high-throughput and speed of the method make it suitable for clinical application. © 2012 Elsevier B.V.
Dai Y.,Peking Union Medical College |
Wei X.,BGI Wuhan |
Zhao Y.,Peking Union Medical College |
Ren H.,Peking Union Medical College |
And 5 more authors.
Neuromuscular Disorders | Year: 2015
Muscular dystrophies and congenital myopathies are a large group of heterogeneous inherited muscle disorders. The spectrum of muscular dystrophies and congenital myopathies extends to more than 50 diseases today, even excluding the common forms Duchenne Muscular Dystrophy, Myotonic Dystrophy and Facioscapulohumeral Dystrophy. Unfortunately, even by critical clinical evaluation and muscle pathology, diagnosis is still difficult. To potentially remediate this difficulty, we applied a microarray-based targeted next-generation sequencing (NGS) technology to diagnose these patients. There were 55 consecutive unrelated patients who underwent the test, 36 of which (65%) were found to have a causative mutation. Our result shows the accuracy and efficiency of next-generation sequencing in clinical circumstances and reflects the features and relative distribution of inherited myopathies in the Chinese population. © 2015 Elsevier B.V..
Liu Y.,Jiangxi Provincial Women and Children Hospital |
Wei X.,BGI Wuhan |
Kong X.,Zhengzhou University |
Guo X.,BGI Wuhan |
And 8 more authors.
PLoS ONE | Year: 2015
Background: Targeted next-generation sequencing (NGS) is a cost-effective approach for rapid and accurate detection of genetic mutations in patients with suspected genetic disorders, which can facilitate effective diagnosis. Methodology/Principal Findings: We designed a capture array to mainly capture all the coding sequence (CDS) of 2,181 genes associated with 561 Mendelian diseases and conducted NGS to detect mutations. The accuracy of NGS was 99.95%, which was obtained by comparing the genotypes of selected loci between our method and SNP Array in four samples from normal human adults. We also tested the stability of the method using a sample from normal human adults. The results showed that an average of 97.79% and 96.72% of single-nucleotide variants (SNVs) in the sample could be detected stably in a batch and different batches respectively. In addition, the method could detect various types of mutations. Some disease-causing mutations were detected in 69 clinical cases, including 62 SNVs, 14 insertions and deletions (Indels), 1 copy number variant (CNV), 1 microdeletion and 2 microduplications of chromosomes, of which 35 mutations were novel. Mutations were confirmed by Sanger sequencing or real-time polymerase chain reaction (PCR). Conclusions/Significance: Results of the evaluation showed that targeted NGS enabled to detect disease-causing mutations with high accuracy, stability, speed and throughput. Thus, the technology can be used for the clinical diagnosis of 561 Mendelian diseases. Copyright: © 2015 Liu et al.
Guo Y.,Central South University |
Yuan J.,Central South University |
Liang H.,Central South University |
Xiao J.,BGI Shenzhen |
And 7 more authors.
Molecular Biology Reports | Year: 2014
Alport syndrome (AS) is an inherited disorder and clinically characterized by glomerulonephritis and end-stage kidney disease (ESRD). The aim of this study was to identify the gene responsible for glomerulopathy in a 4-generation Chinese pedigree. Exome sequencing was conducted in four patients of the family, and then direct sequencing was performed in other members of the pedigree. A novel missense mutation c.368G>A (p.Gly123Glu) in the collagen type IV alpha-5 gene (COL4A5) was found to be the genetic cause. The p.Gly123Glu mutation occurs prior to Gly-X-Y repeats in the alpha-5 chain of type IV collagen. Neither sensorineural hearing loss nor ocular abnormalities were present in patients of this family. Other clinical features, such as age of onset, age of ESRD, disease severity and complications, varied among patients of this family. Our finding may provide new insights into the cause and diagnosis of AS, and also have implications for genetic counseling. © 2014 Springer Science+Business Media.
PubMed | Jiangxi Provincial Women and Children Hospital, Wuhan Medical and Health Center for Women and Children, Zhengzhou University, BGI Wuhan and BGI Shenzhen
Type: Journal Article | Journal: PloS one | Year: 2015
Targeted next-generation sequencing (NGS) is a cost-effective approach for rapid and accurate detection of genetic mutations in patients with suspected genetic disorders, which can facilitate effective diagnosis.We designed a capture array to mainly capture all the coding sequence (CDS) of 2,181 genes associated with 561 Mendelian diseases and conducted NGS to detect mutations. The accuracy of NGS was 99.95%, which was obtained by comparing the genotypes of selected loci between our method and SNP Array in four samples from normal human adults. We also tested the stability of the method using a sample from normal human adults. The results showed that an average of 97.79% and 96.72% of single-nucleotide variants (SNVs) in the sample could be detected stably in a batch and different batches respectively. In addition, the method could detect various types of mutations. Some disease-causing mutations were detected in 69 clinical cases, including 62 SNVs, 14 insertions and deletions (Indels), 1 copy number variant (CNV), 1 microdeletion and 2 microduplications of chromosomes, of which 35 mutations were novel. Mutations were confirmed by Sanger sequencing or real-time polymerase chain reaction (PCR).Results of the evaluation showed that targeted NGS enabled to detect disease-causing mutations with high accuracy, stability, speed and throughput. Thus, the technology can be used for the clinical diagnosis of 561 Mendelian diseases.
PubMed | Nanjing Southeast University, BGI Shenzhen, CAS Institute of Botany, BGI Wuhan and 2 more.
Type: Journal Article | Journal: GigaScience | Year: 2016
Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution.The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways.The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.
PubMed | Shenzhen Maternity and Child Healthcare Hospital and BGI Wuhan
Type: | Journal: BMC medical genetics | Year: 2016
Argininosuccinic aciduria (ASAuria; OMIM 207900) is a rare autosomal recessive heterogeneous urea cycle disorder, which leads to the accumulation of argininosuccinic acid in the blood and urine. We aimed to perform genetic test to the patient and help clinician to diagnose precisely.In this study, we use next generation sequencing (NGS) and exon trapping to analysis the family members. We identified compound heterozygous mutations of the argininosuccinate lyase (ASL) gene in a Chinese Han ASAuria patient. The c.434A>G (p.(D145G)) mutation in exon 5 was shown by exon trapping to select for the formation of an alternative transcript deleted for exon 5. The c.1366C>T (p.(R456W)) mutation had been previously reported in an Italian patient.This is the first report of a missense mutation driving alternative splicing which results in the loss of exon 5 in ASAuria. This study also demonstrates the value of NGS in the identification of mutations and molecular diagnosis for ASAuria families.
PubMed | Shenzhen Childrens Hospital, BGI Wuhan and Shantou University
Type: Case Reports | Journal: Brain & development | Year: 2015
Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is a rare autosomal recessive neuromuscular disorder caused by mutations in the IGHMBP2 gene and characterized by life-threatening respiratory distress due to irreversible diaphragmatic paralysis between 6weeks and 6months of age. In this study, we describe a two-month-old boy who presented with hypertonia at first and developed to hypotonia progressively, which was in contrast to the manifestations reported previously. Bone tissue compromise was also observed as one of the unique symptoms. Muscle biopsy indicated mild myogenic changes. He was misdiagnosed until genetic screening to be confirmed as SMARD1. SMARD1 is a clinical heterogeneous disease and this case broadens our perception of its phenotypes.
Wang X.,Women and Childrens Hospital of Sichuan Province |
Yang Y.,BGI Wuhan |
Zhou R.,University of Sichuan
Experimental and Therapeutic Medicine | Year: 2016
A patient with progressive muscular atrophy was assessed for the disease-associated genes by next-generation sequencing technology and exon trap and sequence analysis. The results of the investigation identified 399 genes, covering all exons in addition to 10 bp on either side, which are specific to 659 types of neuromuscular disorders, including hypotypes. Exon capture and sequence analysis revealed that the patient possessed two splice site mutations in the dysferlin (DYSF) gene, c.144+1G>A and c.342+1G>T, and the presence of the mutations was confirmed by Sanger sequencing. The patient's mother and sister were also assessed and confirmed to have mutations within the DYSF gene, the mother with c.342+1G>T and the sister with c.144+1G>A. The two splice site mutations in the DYSF gene, c.144+1G>A and c.342+1G>T, have not previously been reported. Therefore, exon capture and sequence analysis is able to rapidly and efficiently screen for genetic alterations in neuromuscular disorders. © 2016, Spandidos Publications. All rights reserved.