Array-based sequence capture and next-generation sequencing for the identification of primary immunodeficiencies

Primary immunodeficiencies are genetic disorders in which components of immunological pathways are either missing or dysregulated. With the advent of next-generation sequencing, testing for genes in conditions with a heterogeneous genetic background seems more promising. We designed a custom microarray with 385K probe capacity to capture exons of 395 human genes, known or predicted to be associated with primary immunodeficiency and immune regulation. Enriched target DNA was sequenced using a GS FLX Titanium 454 platform. The patients selected were likely to have an underlying immunodeficiency. In one patient with hepatosplenomegaly, recurrent infections and an elevated IgM level, sequence analysis of the patient and his two unaffected parents identified ATM (ataxia telangiectasia mutated) as the underlying defect. In a second child with a clinical SCID phenotype, we detected a mutation in the ARTEMIS gene after focusing on SCID-associated genes. 454 sequencing yielded 152,000-397,000 high-quality reads per patient. 78-99% of the targeted nucleotides were covered at least one time, 76-82% at least five times. Array-based sequence capture expands our capacities to sequence large targeted DNA regions in a less laborious and time-consuming approach. Our array was capable to find the underlying genetic defect in two patients with suspected primary immunodeficiency. Upcoming whole-exome sequencing definitely will add more valuable data, but bioinformatical analysis and validation of variants already pose major challenges.     

Guidelines for diagnostic next-generation sequencing

We present, on behalf of EuroGentest and the European Society of Human Genetics, guidelines for the evaluation and validation of next-generation sequencing (NGS) applications for the diagnosis of genetic disorders. The work was performed by a group of laboratory geneticists and bioinformaticians, and discussed with clinical geneticists, industry and patients'' representatives, and other stakeholders in the field of human genetics. The statements that were written during the elaboration of the guidelines are presented here. The background document and full guidelines are available as supplementary material. They include many examples to assist the laboratories in the implementation of NGS and accreditation of this service. The work and ideas presented by others in guidelines that have emerged elsewhere in the course of the past few years were also considered and are acknowledged in the full text. Interestingly, a few new insights that have not been cited before have emerged during the preparation of the guidelines. The most important new feature is the presentation of a ‘rating system'' for NGS-based diagnostic tests. The guidelines and statements have been applauded by the genetic diagnostic community, and thus seem to be valuable for the harmonization and quality assurance of NGS diagnostics in Europe.Next-generation sequencing (NGS) allows for the fast generation of thousands to millions of base pairs of DNA sequence of an individual patient. The relatively fast emergence and the great success of these technologies in research herald a new era in genetic diagnostics. However, the new technologies bring challenges, both at the technical level and in terms of data management, as well as for the interpretation of the results and for counseling. We believe that all these aspects warrant consideration of what the precise role of NGS in diagnostics will be, today and tomorrow. Before even embarking on acquisition of machines and skills for performing NGS in diagnostics, many issues have to be dealt with. It is in this context that we propose the guidelines. These guidelines mostly deal with NGS testing in the context of rare and mostly monogenic diseases. They mainly focus on the targeted analysis of gene panels, either through specific capture assays, or by extracting data from whole-exome sequencing. In principle, whole-genome sequencing may – and shortly will – also be used to extract similar information. In that case, the guidelines would still apply, but because whole-genome sequencing would also allow detecting other molecular features of disease, they would have to be extended accordingly.The different aspects of NGS and diagnostics were discussed during three workshops. The first took place in Leuven, 25–26 February 2013. The preliminary views were presented during the EuroGentest Scientific Meeting in Prague, 7–8 March 2013. The second was an editorial workshop in Leuven, 1–2 October 2013, where the different people involved in writing the document came together to discuss the layout of the document and prepare the first draft. The first draft was finalized prior to the third meeting in Nijmegen, 21–22 November, 2013. To the latter meeting, a larger group of stakeholders was invited. They were invited to comment on the draft, and on the statements presented therein. The comments were included in a new version, which was circulated among the editorial group, prior to publication on the EuroGentest and European Society of Human Genetics websites. Eventually, the document was presented to the Board of the European Society of Human Genetics, for endorsement. Endorsement was formally obtained on 1 July 2015.The statements that emerged during the writing of the guidelines are briefly presented in this paper. They are more extensively explained in the full version of the guidelines, available as supplementary material. The supplementary material also includes definitions, general recommendations and importantly, a number of practical examples and templates.     

National external quality assessment for next-generation sequencing-based diagnostics of primary immunodeficiencies

Dutch genome diagnostic centers (GDC) use next-generation sequencing (NGS)-based diagnostic applications for the diagnosis of primary immunodeficiencies (PIDs). The interpretation of genetic variants in many PIDs is complicated because of the phenotypic and genetic heterogeneity. To analyze uniformity of variant filtering, interpretation, and reporting in NGS-based diagnostics for PID, an external quality assessment was performed. Four main Dutch GDCs participated in the quality assessment. Unannotated variant call format (VCF) files of two PID patient analyses per laboratory were distributed among the four GDCs, analyzed, and interpreted (eight analyses in total). Variants that would be reported to the clinician and/or advised for further investigation were compared between the centers. A survey measuring the experiences of clinical laboratory geneticists was part of the study. Analysis of samples with confirmed diagnoses showed that all centers reported at least the variants classified as likely pathogenic (LP) or pathogenic (P) variants in all samples, except for variants in two genes (PSTPIP1 and BTK). The absence of clinical information complicated correct classification of variants. In this external quality assessment, the final interpretation and conclusions of the genetic analyses were uniform among the four participating genetic centers. Clinical and immunological data provided by a medical specialist are required to be able to draw proper conclusions from genetic data.Subject terms: Medical research, Immunology     

Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing

Translocations are a common class of chromosomal aberrations and can cause disease by physically disrupting genes or altering their regulatory environment. Some translocations, apparently balanced at the microscopic level, include deletions, duplications, insertions, or inversions at the molecular level. Traditionally, chromosomal rearrangements have been investigated with a conventional banded karyotype followed by arduous positional cloning projects. More recently, molecular cytogenetic approaches using fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH), or whole-genome SNP genotyping together with molecular methods such as inverse PCR and quantitative PCR have allowed more precise evaluation of the breakpoints. These methods suffer, however, from being experimentally intensive and time-consuming and of less than single base pair resolution. Here we describe targeted breakpoint capture followed by next-generation sequencing (TBCS) as a new approach to the general problem of determining the precise structural characterization of translocation breakpoints and related chromosomal aberrations. We tested this approach in three patients with complex chromosomal translocations: The first had craniofacial abnormalities and an apparently balanced t(2;3)(p15;q12) translocation; the second has cleidocranial dysplasia (OMIM 119600) associated with a t(2;6)(q22;p12.3) translocation and a breakpoint in RUNX2 on chromosome 6p; and the third has acampomelic campomelic dysplasia (OMIM 114290) associated with a t(5;17)(q23.2;q24) translocation, with a breakpoint upstream of SOX9 on chromosome 17q. Preliminary studies indicated complex rearrangements in patients 1 and 3 with a total of 10 predicted breakpoints in the three patients. By using TBCS, we quickly and precisely defined eight of the 10 breakpoints.     

Spectrum of mutations in leiomyosarcomas identified by clinical targeted next-generation sequencing

Recurrent genomic mutations in uterine and non-uterine leiomyosarcomas have not been well established. Using a next generation sequencing (NGS) panel of common cancer-associated genes, 25 leiomyosarcomas arising from multiple sites were examined to explore genetic alterations, including single nucleotide variants (SNV), small insertions/deletions (indels), and copy number alterations (CNA). Sequencing showed 86 non-synonymous, coding region somatic variants within 151 gene targets in 21 cases, with a mean of 4.1 variants per case; 4 cases had no putative mutations in the panel of genes assayed. The most frequently altered genes were TP53 (36%), ATM and ATRX (16%), and EGFR and RB1 (12%). CNA were identified in 85% of cases, with the most frequent copy number losses observed in chromosomes 10 and 13 including PTEN and RB1; the most frequent gains were seen in chromosomes 7 and 17. Our data show that deletions in canonical cancer-related genes are common in leiomyosarcomas. Further, the spectrum of gene mutations observed shows that defects in DNA repair and chromosomal maintenance are central to the biology of leiomyosarcomas, and that activating mutations observed in other common cancer types are rare in leiomyosarcomas.     

应用下一代半导体靶向测序技术检测Marfan综合征致病突变

目的 应用Ion Torrent PGM半导体测序仪和Ion AmpliSeqTMInherited Disease Panel对3例马凡综合征(Marfan syndrome,MFS)进行致病基因突变检测,明确其致病突变,并评价下一代半导体靶向测序诊断复杂单基因遗传病的效果.方法 在知情同意的基础上采集3例MFS患者及1名正常志愿者外周血,提取基因组DNA,经多重PCR扩增富集目的基因片段.每个样本用特异性序列标签进行标记后,应用Ion One Touch系统进行模板制备、乳化PCR及磁珠颗粒富集;最后用318半导体测序芯片进行高通量测序.用Ion Torrent Suite 3.2软件进行序列比对及SNPs和Indels提取,再用dbSNP 137数据库过滤得到SNPs和indels,剩余的可疑突变经Sanger法测序验证.结果 用一张318芯片得到855.80Mb的总数据量,4个样本的平均测序深度均达到100×以上,对目的区域的覆盖度在98％以上.数据经软件分析及数据库过滤后,在3例MFS患者中分别得到3个FBN1基因可疑突变,并经Sanger法测序验证,一个为已报道FBN1基因错义突变(p.E1811K),另外两个为新发现的突变,包括一个无义突变(p.E2264X),1个插入突变(p.L871FfsX23).结论 在3例MFS患者中都成功检出FBN1基因致病突变,表明半导体靶向测序可对复杂单基因遗传病进行高效、准确的基因诊断.     

A mild form of Mucopolysaccharidosis IIIB diagnosed with targeted next-generation sequencing of linked genomic regions

Next-generation sequencing (NGS) techniques have already shown their potential in the identification of mutations underlying rare inherited disorders. We report here the application of linkage analysis in combination with targeted DNA capture and NGS to a Norwegian family affected by an undiagnosed mental retardation disorder with an autosomal recessive inheritance pattern. Linkage analysis identified two loci on chromosomes 9 and 17 which were subject to target enrichment by hybridization to a custom microarray. NGS achieved 20-fold or greater sequence coverage of 83% of all protein-coding exons in the target regions. This led to the identification of compound heterozygous mutations in NAGLU, compatible with the diagnosis of Mucopolysaccharidosis IIIB (MPS IIIB or Sanfilippo Syndrome type B). This diagnosis was confirmed by demonstrating elevated levels of heparan sulphate in urine and low activity of α-N-acetyl-glucosaminidase in cultured fibroblasts. Our findings describe a mild form of MPS IIIB and illustrate the diagnostic potential of targeted NGS in Mendelian disease with unknown aetiology.     

Contribution of high‐throughput DNA sequencing to the study of primary immunodeficiencies

Primary immunodeficiencies (PIDs) are inborn errors of the immune system. PIDs have been characterized immunologically for the last 60 years and genetically, principally by Sanger DNA sequencing, over the last 30 years. The advent of next‐generation sequencing (NGS) in 2011, with the development of whole‐exome sequencing in particular, has facilitated the identification of previously unknown genetic lesions. NGS is rapidly generating a stream of candidate variants for an increasing number of genetically undefined PIDs. The use of NGS technology is ushering in a new era, by facilitating the discovery and characterization of new PIDs in patients with infections and other phenotypes, thereby helping to improve diagnostic accuracy. This review provides a historical overview of the identification of PIDs before NGS, and the advances and limitations of the use of NGS for the diagnosis and characterization of PIDs.     

Pathway analysis with next-generation sequencing data

Although pathway analysis methods have been developed and successfully applied to association studies of common variants, the statistical methods for pathway-based association analysis of rare variants have not been well developed. Many investigators observed highly inflated false-positive rates and low power in pathway-based tests of association of rare variants. The inflated false-positive rates and low true-positive rates of the current methods are mainly due to their lack of ability to account for gametic phase disequilibrium. To overcome these serious limitations, we develop a novel statistic that is based on the smoothed functional principal component analysis (SFPCA) for pathway association tests with next-generation sequencing data. The developed statistic has the ability to capture position-level variant information and account for gametic phase disequilibrium. By intensive simulations, we demonstrate that the SFPCA-based statistic for testing pathway association with either rare or common or both rare and common variants has the correct type 1 error rates. Also the power of the SFPCA-based statistic and 22 additional existing statistics are evaluated. We found that the SFPCA-based statistic has a much higher power than other existing statistics in all the scenarios considered. To further evaluate its performance, the SFPCA-based statistic is applied to pathway analysis of exome sequencing data in the early-onset myocardial infarction (EOMI) project. We identify three pathways significantly associated with EOMI after the Bonferroni correction. In addition, our preliminary results show that the SFPCA-based statistic has much smaller P-values to identify pathway association than other existing methods.     

Long-term follow-up of patients with primary immunodeficiencies

As an example of the need for long-term follow-up by specialty health care to adequately manage immunodeficient patients, we report the case of a patient with Wiskott-Aldrich syndrome who was lost to follow-up for 4 years to the immunology clinic and came back with a neck mass that was diagnosed as B-cell lymphoma. Patients with immunodeficiency are at high risk for the development of malignancy and autoimmune diseases and should be evaluated by a trained specialist with a frequency of not less than every 6 months.     

Pathogenic gene screening in 91 Chinese patients with short stature of unknown etiology with a targeted next-generation sequencing panel

Background

Dwarfism is a common severe growth disorder, but the etiology is unclear in the majority of cases. Recombinant human growth hormone may be a treatment option, but it has limited efficacy. The currently known laboratory assays do not meet the precision requirements for clinical diagnosis. Here, we have constructed a targeted next-generation sequencing (NGS) panel of selected genes that are suspected to be associated with dwarfism for genetic screening.

Methods

Genetic screening of 91 children with short stature of unknown etiology was performed with the help of the NGS panel. All the coding regions and exon-intron boundaries of 166 genes were included in the panel. To clarify the pathogenicity of these mutations, their clinical data were reviewed and analyzed.

Results

The assay identified p.A72G, p.I282V, and p.P491S variants of the PTPN11 gene and a p.I437T variant of the SOS1 gene in 4 cases with Noonan syndrome. A frameshift mutation (p.D2407fs) of the ACAN gene was identified in a case of idiopathic short stature with moderately advanced bone age. A p.R904C variant of the COL2A1 gene was found in a patient, who was accordingly diagnosed with Stickler syndrome. Severe short stature without limb deformity was associated with a p.G11A variant of HOXD13. In addition, we evaluated evidence that a p.D401N variant of the COMP gene may cause multiple epiphyseal dysplasia.

Conclusions

Our findings suggest that syndromes, particularly Noonan syndrome, may be overlooked due to atypical clinical features. This gene panel has been verified to be effective for the rapid screening of genetic etiologies associated with short stature and for guiding precision medicine-based clinical management.

     

Infectious complications of the primary immunodeficiencies

The primary manifestation of the immunodeficiencies is undue susceptibility to infection. This means too many, too severe, too prolonged, too complicated and too unusual infections. Infections in immunodeficiency have a characteristic cause depending on the nature of the immune deficiency. Antibody deficiencies are associated with infections with gram-positive infections. Cellular immune deficiencies are associated with mycobacterial, protozoan, fungus, virus, and opportunistic bacterial infection. Phagocytic disorders are associated with staphylococcal, fungal, and gram-negative organisms. Complement disorders are associated by neisserial infections. Infections have also been implicated in the pathogenesis of some immunodeficiencies in some circumstances. These include human T lymphotropic virus type III (HTLV-III), rubella virus, cytomegalovirus, and Epstein-Barr virus. Several infectious syndromes in specific immunodeficiencies have been identified. Examples include enteric cytopathic human orphan (ECHO) virus encephalitis in agammaglobulinemia, and meningococcal meningitis in C6 deficiency. Infections can also be induced by live vaccines given in immunodeficiency (e.g., paralytic polio in agammaglobulinemia.) Unusual infectious syndromes will be illustrated including parainfluenza infection in severe combined and immunodeficiency, Legionella pneumonia in chronic granulomatous disease, and Cryptosporidium infection in hyper-IgM immunodeficiency.     

The first patient with sporadic X-linked intellectual disability with de novo ZDHHC9 mutation identified by targeted next-generation sequencing

X-linked intellectual disability (XLID) is a genetically heterogeneous disorder involving more than 100 genes known to date. Here, we describe a Korean male infant with global developmental delay. He had neither facial dysmorphism nor skeletal abnormalities. Bayley scale of infant and toddler development third edition (Bayley-III) measured at age of 2 years revealed marked global developmental delays without Marfanoid habitus, structural brain abnormalities, or epilepsy. The patient's cognitive, motor, and language developmental ages were 8–9 months, 12 months, and 9 months, respectively. Targeted next-generation sequencing revealed a de novo mutation [NM_001008222.2(ZDHHC9): c.286C > T (p.(Arg96Trp))] in the affected patient. This mutation has been reported previously in a family XLID with Marfanoid features. Sanger sequencing analysis of the proband and his parents revealed that the missense mutation was present in the proband only (absent in his parents). This indicates that the mutation is de novo in origin. To the best of our knowledge, this is the first report describing sporadic XLID with de novo ZDHHC9 mutation identified by targeted next-generation sequencing.