Pathogenicity and selective constraint on variation near splice sites.

Mutations that perturb normal pre-mRNA splicing are significant contributors to human disease. We used exome sequencing data from 7833 probands with developmental disorders (DDs) and their unaffected parents, as well as more than 60,000 aggregated exomes from the Exome Aggregation Consortium, to investigate selection around the splice sites and quantify the contribution of splicing mutations to DDs. Patterns of purifying selection, a deficit of variants in highly constrained genes in healthy subjects, and excess de novo mutations in patients highlighted particular positions within and around the consensus splice site of greater functional relevance.

Detection of structural mosaicism from targeted and whole-genome sequencing data.

Structural mosaic abnormalities are large post-zygotic mutations present in a subset of cells and have been implicated in developmental disorders and cancer. Such mutations have been conventionally assessed in clinical diagnostics using cytogenetic or microarray testing. Modern disease studies rely heavily on exome sequencing, yet an adequate method for the detection of structural mosaicism using targeted sequencing data is lacking.

Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing.

Congenital heart defects (CHDs) have a neonatal incidence of 0.8-1% (refs. 1,2).

Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families.

Discovery of most autosomal recessive disease-associated genes has involved analysis of large, often consanguineous multiplex families or small cohorts of unrelated individuals with a well-defined clinical condition. Discovery of new dominant causes of rare, genetically heterogeneous developmental disorders has been revolutionized by exome analysis of large cohorts of phenotypically diverse parent-offspring trios. Here we analyzed 4,125 families with diverse, rare and genetically heterogeneous developmental disorders and identified four new autosomal recessive disorders.

Phenotypic diversity in the Smith-Lemli-Opitz syndrome.

The phenotype of four cases of Smith-Lemli-Opitz syndrome (SLO) with proven defects in cholesterol biosynthesis are compared, and shown to be markedly disparate even between sibs, and demonstrate the dilemma for the clinician. The advent of a biochemical test for SLO has been enormously valuable in determining which patients are truly affected by the condition, but because of the wide phenotypic variation, a diagnosis on clinical features alone remains problematic.

A new lethal chondrodysplasia with platyspondyly, long bone angulation and mixed bone density.

A fetus diagnosed by sonography at 20 weeks' gestation had multiple skeletal abnormalities. The main features were absent ossification of the skull and cervical and upper thoracic vertebral bodies; short, angulated femora, tibiae, radii and ulnae but normal humeri; platyspondyly; trident-shaped acetabular roofs; sclerotic bands on the iliac wings and scapulae; clavicular hooks; and overall, mixed bone density. We suggest that this is a new chondrodysplasia which, since the parents are first cousins, could follow autosomal recessive inheritance.

A fetus with an X;1 balanced reciprocal translocation and eye disease.

A 19 week female fetus is described with a de novo X;1 reciprocal balanced translocation, with the breakpoint on the X chromosome at Xp11.4, and eye pathology consistent with the early stages of Norrie disease. The fetus seems to be an example of a female manifesting an X linked recessive disease, and it was shown that the normal X chromosome was completely inactivated in all cells examined.

A fetus with an abnormal chromosome 7 and possible hydrolethalus syndrome.

A fetus with multiple abnormalities phenotypically similar to hydrolethalus syndrome, but also with broad thumbs, was found to have a de novo interstitial deletion of the terminal segment of the long arm of chromosome 7 and a small rearrangement within the proximal half of the p arm of the same chromosome. Terminal deletions of chromosome 7q fall into two broad phenotypic groups, neither of which resembles this fetus, but the digital anomalies are attributed to the 7p rearrangement disrupting the Greig syndrome gene.

Pseudotrisomy 13 and autosomal recessive holoprosencephaly.

Two sibs, diagnosed prenatally, had holoprosencephaly, midface hypoplasia, and normal chromosomes. The first fetus also had polydactyly. This sibship may represent an example of autosomal recessive pseudotrisomy 13.

Grief and mid-trimester fetal loss.

Fetal loss through miscarriage or termination of pregnancy for genetic reasons often provokes the grief of bereavement. This is not fully understood, and the extent of the distress is often underestimated by professionals and family alike. We have examined elements of the normal bereavement process and have found that they may occur in specific and accentuated forms in mid-trimester fetal loss.

PRUFILE: a clinical and laboratory database for the genetics centre.

The growing complexity and volume of workload in a Clinical Genetics Centre can rapidly swamp the available clerical facilities. The multiuser database described gives facilities not only for administrative control and documentation but also for the production of data for clinical and scientific analysis. The close link between clinical and laboratory databases gives great versatility and easy expansion as new tests and disciplines are applied to clinical genetic problems.