全外显子组测序在常染色体隐性遗传病致病基因克隆中的应用策略

全外显子组测序(whole-exome sequencing,WES)是近年发展起来的一种先应用靶向富集技术捕获基因组的外显子区域,再通过高通量测序获得编码区序列遗传信息的分析技术.该技术目前已被广泛应用于孟德尔单基因遗传病,特别是常染色体隐性遗传病的基因克隆.作者对近期全外显子组测序技术在常染色体隐性遗传病致病基因克隆中的应用策略进展进行了综述.     

The use of whole exome sequencing for the diagnosis of autosomal recessive malignant infantile osteopetrosis

Autosomal recessive malignant infantile osteopetrosis is a congenital disease characterized by pathologically increased bone density. Recently, the use of whole exome sequencing has been utilized as a clinical diagnostic tool in a number of Mendelian disorders. In this study, whole exome sequencing (WES) was successfully used in six patients with malignant infantile osteopetrosis (MIOP) and identified mutations in four MIOP‐related genes (CLCN7, TCIRG1, SNX10, and TNFRSF11A). We report these patients, describe the mutations and review the current literature.     

Novel mutations in typical and atypical genetic loci through exome sequencing in autosomal recessive cerebellar ataxia families

Nearly a thousand mutations mapping to 60 different loci have been identified in cerebellar ataxias. However, almost 50% of the cases remain genetically uncharacterized and there is a difference in prevalence as well as in the phenotypic spectrum of ataxia among various geographical regions. This poses a challenge for setting up a genetic panel for screening ataxia. In our ataxic cohort of 1014 families, 61% are genetically uncharacterized (UC). We investigated the potential of whole exome sequencing in conjunction with homozygosity mapping (HM) to delineate the genetic defects in three uncharacterized families with recessive inheritance each manifesting some unusual phenotype: (i) infantile onset ataxia with hearing loss (IOAH), (ii) Juvenile onset cerebellar ataxia with seizures (JCS) and (iii) Friedreich ataxia‐like (FA‐like). We identified a novel missense mutation in c10orf2 in the family with IOAH, compound heterozygous mutations in CLN6 in the family with JCS and a homozygous frame‐shift mutation in SACS in the FA‐like patient. Phenotypes observed in our families were concordant with reported phenotypes of known mutations in the same genes thus obviating the need for functional validation. Our study revealed novel variations in three genes, c10orf2, CLN6, and SACS, that have so far not been reported in India. This study also demonstrates the utility of whole exome screening in clinics for early diagnosis.     

Shadow autozygosity mapping by linkage exclusion (SAMPLE): a simple strategy to identify the genetic basis of lethal autosomal recessive disorders

Autozygosity mapping has been invaluable for determining the genetic basis of lethal autosomal recessive disorders, but this approach remains challenging because DNA from affected individuals may often be unavailable or of insufficient quality for extensive molecular genetic studies. To circumvent these difficulties, we developed a computer program called “SAMPLE” (for s hadow a utozygosity m ap ping by l inkage e xclusion) to enhance autozygosity mapping through the empirical analysis of haplotypes of unaffected individuals in consanguineous families. Single nucleotide polymorphism (SNP) genotyping of unaffected individuals in complex consanguineous pedigrees is used to infer limited chromosomal regions compatible with linkage to a potential disease locus, and to allow the immediate prioritization of potential regions of interest. Further limited genotyping then enables the rapid confirmation and fine mapping of a disease locus. We demonstrate the utility of this strategy by using genotyping data from only parents and unaffected siblings, in three consanguineous families affected with Meckel-Gruber syndrome, to correctly infer the location of the MKS3/TMEM67 locus on chromosome 8q22.1. This strategy is practicable only with the recent advances in whole genome genotyping by high-density SNP microarrays, and could not be easily implemented in approaches that rely on microsatellite markers. SAMPLE is available at http://dna.leeds.ac.uk/sample/ . Hum Mutat 30:1–8, 2009. © 2009 Wiley-Liss, Inc.     

A lethal autosomal recessive entero-colitis of early infancy

A family is presented in which three of four children died with an almost identical syndrome. It started within a week or so of birth and presented as bloody diarrhea with a very swollen abdomen. All died after some weeks: autopsy revealed ulcerative colitis in two and pseudo-membranous entero-colitis in the third. The parents were second cousins There may have been a milk intolerance. The disease is apparently due to an autosomal recessive gene.     

Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort

PurposeAutosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity, with reported mutations in 58 different genes. This study was designed to detect deafness-causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES).MethodsAfter excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador, and Puerto Rico to screen for mutations in all known ARNSD genes.ResultsWe detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%), and CDH23 (4%). Nine mutations were detected in multiple families with shared haplotypes, suggesting founder effects.ConclusionWe report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families.     

A new autosomal recessive lethal chondrodystrophy with congenital hydrops

Two sibs, the offspring of consanguineous parents, presented with severe short-limb dwarfism and distinct chondro-osseous, radiologic, and histologic appearance. The first sib presented at 30 wk with severe hydrops following fetal death; the second was detected by ultrasonography at 20 wk. Radiologic abnormalities included an unusual "moth-eaten" appearance of the markedly short long bones, bizzare ectopic ossification centers, and marked platyspondyly with unusual ossification centers. Marked extramedullary erythropoiesis was present in both fetuses, and chondro-osseous histology was characterized by marked disorganization of tissue with interspersed masses of cartilage, bone, and mesenchymal tissue. These sibs appear to have a distinct previously unreported autosomal recessive skeletal dysplasia, which can present as hydrops fetalis.     

A lethal autosomal recessive syndrome of multiple congenital contractures

We describe 16 cases of a lethal syndrome with multiple congenital contractures from ten families. The main clinical findings included intrauterine growth retardation with marked fetal hydrops, multiple contractures, and facial abnormalities, especially micrognathia. At autopsy, pulmonary hypoplasia and muscular atrophy were present. There was a paucity of anterior horn motor neurons in the four studied cases. We think that the cases represent the same clinical entity, probably caused by homozygosity of an autosomal recessive gene. The syndrome resembles the Pena-Shokeir I syndrome, but seems to differ in some respects, including length of survival and presence of hydrops. Prenatal diagnosis of this syndrome is possible after the 16th week of pregnancy with ultrasound.     

Using next-generation sequencing as a genetic diagnostic tool in rare autosomal recessive neurologic Mendelian disorders

Next-generation sequencing was used to investigate 9 rare Chinese pedigrees with rare autosomal recessive neurologic Mendelian disorders. Five probands with ataxia-telangectasia and 1 proband with chorea-acanthocytosis were analyzed by targeted gene sequencing. Whole-exome sequencing was used to investigate 3 affected individuals with Joubert syndrome, nemaline myopathy, or spastic ataxia Charlevoix-Saguenay type. A list of known and novel candidate variants was identified for each causative gene. All variants were genetically verified by Sanger sequencing or quantitative polymerase chain reaction with the strategy of disease segregation in related pedigrees and healthy controls. The advantages of using next-generation sequencing to diagnose rare autosomal recessive neurologic Mendelian disorders characterized by genetic and phenotypic heterogeneity are demonstrated. A genetic diagnostic strategy combining the use of targeted gene sequencing and whole-exome sequencing with the aid of next-generation sequencing platforms has shown great promise for improving the diagnosis of neurologic Mendelian disorders.     

Lifting the lid on unborn lethal Mendelian phenotypes through exome sequencing

PurposeMendelian phenotypes in humans vary from benign variants to lethal disorders. Embryonic lethal phenotypes that are similar to what has been known for a long time in mice have remained largely unknown because of the difficulty in arriving at a molecular diagnosis. The purpose of this study is to test whether next generation sequencing can reveal the underlying etiology of recurrent fetal loss.MethodsWe hypothesized that exome sequencing combined with autozygome analysis can reveal the underlying mutation in a family in which recurrent fetal loss was likely to be autosomal recessive in origin.ResultsA novel mutation in CHRNA1 was identified. This gene is known to cause multiple pterygium and fetal akinesia syndrome.ConclusionThis is the first report of exome sequencing to identify the cause of recurrent fetal loss and reveal the diagnosis of a lethal human phenotype. Our results should inspire a systematic examination of the extent of “unborn” Mendelian phenotypes in humans using next-generation sequencing.Genet Med 2013:15(4):307–309     

Exome sequencing identifies mutations in KIF14 as a novel cause of an autosomal recessive lethal fetal ciliopathy phenotype

Gene discovery using massively parallel sequencing has focused on phenotypes diagnosed postnatally such as well‐characterized syndromes or intellectual disability, but is rarely reported for fetal disorders. We used family‐based whole‐exome sequencing in order to identify causal variants for a recurrent pattern of an undescribed lethal fetal congenital anomaly syndrome. The clinical signs included intrauterine growth restriction (IUGR), severe microcephaly, renal cystic dysplasia/agenesis and complex brain and genitourinary malformations. The phenotype was compatible with a ciliopathy, but not diagnostic of any known condition. We hypothesized biallelic disruption of a gene leading to a defect related to the primary cilium. We identified novel autosomal recessive truncating mutations in KIF14 that segregated with the phenotype. Mice with autosomal recessive mutations in the same gene have recently been shown to have a strikingly similar phenotype. Genotype–phenotype correlations indicate that the function of KIF14 in cell division and cytokinesis can be linked to a role in primary cilia, supported by previous cellular and model organism studies of proteins that interact with KIF14. We describe the first human phenotype, a novel lethal ciliary disorder, associated with biallelic inactivating mutations in KIF14. KIF14 may also be considered a candidate gene for allelic viable ciliary and/or microcephaly phenotypes.     

Congenital lethal metaphyseal chondrodysplasia: A newly recognized complex autosomal recessive disorder

This is a report of two brothers, born within a year of each other, with a similar skeletal disorder of severe congenital metaphyseal involvement, mild rhizomelic shortness of upper limbs, and mild platyspondyly. Both died at three days of cardio-respiratory insufficiency, but only one had ante-mortem lab tests which showed low calcium, high phosphorus, and high alkaline phosphatase levels attributed to a renal defect. On autopsy this same infant was found to have pulmonary, renal and adrenal hemorrhage, and subendocardial myocarditis and myocardial necrosis. The pathogenetic relationship between these manifestations is presently unclear; however, since parents are normal and recently had an affected baby girl, it is presumed that this disorder is an autosomal recessive trait.     

Whole exome and targeted gene sequencing to detect pathogenic recessive variants in early onset cerebellar ataxia

Over 100 genetically distinct causal known loci for hereditary ataxia phenotype poses a challenge for diagnostic work-up for ataxia patients in a clinically relevant time and precision. In the present study using next-generation sequencing, we have investigated pathogenic variants in early-onset cerebellar ataxia cases using whole exome sequencing in singleton/family-designed and targeted gene-panel sequencing. A total of 98 index patients were clinically and genetically (whole exome sequencing (WES) in 16 patients and targeted gene panel of 41 ataxia causing genes in 82 patients) evaluated. Four families underwent WES in family based design. Overall, we have identified 24 variants comprising 20 pathogenic and four likely-pathogenic both rare/novel, variations in 21 early onset cerebellar ataxia patients. Among the identified variations, SACS (n = 7) and SETX (n = 6) were frequent, while ATM (n = 2), TTPA (n = 2) and other rare loci were observed. We have prioritized novel pathogenic variants in RARS2 and FA2H loci through family based design in two out of four families.     

Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders

Recent breakthroughs in exome-sequencing technology have made possible the identification of many causal variants of monogenic disorders. Although extremely powerful when closely related individuals (eg, child and parents) are simultaneously sequenced, sequencing of a single case is often unsuccessful due to the large number of variants that need to be followed up for functional validation. Many approaches filter out common variants above a given frequency threshold (eg, 1%), and then prioritize the remaining variants according to their functional, structural and conservation properties. Here we present methods that leverage the genetic structure across different populations to improve filtering performance while accounting for the finite sample size of the reference panels. We show that leveraging genetic structure reduces the number of variants that need to be followed up by 16% in simulations and by up to 38% in empirical data of 20 exomes from individuals with monogenic disorders for which the causal variants are known.     

Sclerosteosis — An autosomal recessive disorder

Sclerosteosis is a rare, potentially lethal skeletal disorder in which massive bony over-growth leads to facial distortion, cranial nerve compression and progressive rise in intracranial pressure. Gigantism and syndactyly of the 2nd and 3rd fingers are associated features. In a nationwide investigation in South Africa, 25 affected individuals in 15 Afrikaner kindreds have been studied. The minimum prevalence of the contition in this community is 1 in 75,000. Analysis of pedigree data confirms that sclerosteosis is an autosomal recessive condition. The gene frequency in the Afrikaner people is estimated at 0.0035, with 10,000 clinically normal heterozygotes in this population. Heterozygote detection may be possible on a basis of recognition of minor changes which are apparent on skull radiographs.     

Idiopathic haemochromatosis: An autosomal recessive disease

A genetic analysis of 96 pedigrees has confirmed our previously published report and demonstrated an autosomal recessive mode of inheritance for idiopathic haemochromatosis.
Three generations have been analyzed in each family: the sibship of the patient; the parents of the patient; the offspring of the patient. All the data are consistent with a recessive autosomal transmission: (1) An increased rate of consanguineous matings was found among the parents of the patients. (2) Not a single patient having the disease (latent or manifat) was found among either the parents or the children of the probands. (3) Three distinct levels of iron stores - normal, slightly increased and heavily overloaded - have been statistically separated in the haemochroma-totic families. (4) The result of a segregation analysis has shown a percentage of parsom with heavy iron overloads per sibship corresponding to that expected for a recessive autosomal transmission, taking into account a penetrance of 0.20 in the female (the estimate used in this study).