Genome-wide sequencing and the clinical diagnosis of genetic disease: The CAUSES study.

Genome-wide sequencing (GWS) is a standard of care for diagnosis of suspected genetic disorders, but the proportion of patients found to have pathogenic or likely pathogenic variants ranges from less than 30% to more than 60% in reported studies. It has been suggested that the diagnostic rate can be improved by interpreting genomic variants in the context of each affected individual's full clinical picture and by regular follow-up and reinterpretation of GWS laboratory results. Trio exome sequencing was performed in 415 families and trio genome sequencing in 85 families in the CAUSES study. The variants observed were interpreted by a multidisciplinary team including laboratory geneticists, bioinformaticians, clinical geneticists, genetic counselors, pediatric subspecialists, and the referring physician, and independently by a clinical laboratory using standard American College of Medical Genetics and Genomics (ACMG) criteria. Individuals were followed for an average of 5.1 years after testing, with clinical reassessment and reinterpretation of the GWS results as necessary. The multidisciplinary team established a diagnosis of genetic disease in 43.0% of the families at the time of initial GWS interpretation, and longitudinal follow-up and reinterpretation of GWS results produced new diagnoses in 17.2% of families whose initial GWS interpretation was uninformative or uncertain. Reinterpretation also resulted in rescinding a diagnosis in four families (1.9%). Of the families studied, 33.6% had ACMG pathogenic or likely pathogenic variants related to the clinical indication. Close collaboration among clinical geneticists, genetic counselors, laboratory geneticists, bioinformaticians, and individuals' primary physicians, with ongoing follow-up, reanalysis, and reinterpretation over time, can improve the clinical value of GWS.

A hemizygous SCO2 mutation in an early onset rapidly progressive, fatal cardiomyopathy.

Mutations in SCO2, a metallochaperone involved in mitochondrial copper delivery, are associated with early onset, fatal hypertrophic cardiomyopathy. All reported patients carry at least one copy of the common 1541G>A (E140K) mutation. Whereas patients with one copy of the E140K allele, in combination with a more deleterious mutation, follow a severe clinical course, patients homozygous for the E140K mutation have a delayed onset of disease and a more prolonged survival. Here, we have investigated a patient who appeared homozygous for the common 1541G>A mutation based on DNA sequencing and restriction enzyme analysis of a PCR product, yet presented with early onset, severe cardiomyopathy. Restriction enzyme analysis of parental DNA revealed that the mother was heterozygous for 1541G>A, while the father was homozygous wild-type. The patient showed biparental inheritance for microsatellite markers spanning the length of chromosome 22, making isodisomy unlikely. Sequencing of several single nucleotide polymorphisms within the 5'-UTR, intron and single exon of the SCO2 gene was uninformative; however, a 16 bp deletion within the intron was present in the patient and the mother, but not the father. Restriction enzyme analysis confirmed that the mother was heterozygous and that the patient was hemizygous for the deletion. Southern blot, Northern blot, and FISH analyses were consistent with the de novo deletion of one allele of SCO2 in the patient. This is the first report of hemizygosity in a SCO2 patient. The patient phenotype underscores the strikingly similar clinical course in all patients with one copy of the E140K allele. Examination of both patient and parental genotypes by thorough molecular analyses can reveal information with important implications for genetic counseling.

Long-term follow-up of three individuals with Kabuki syndrome.

Long-term follow-up of three individuals with Kabuki syndrome indicates their phenotype becomes less striking as adults. It is characterized by short stature, obesity, and relatively large head. Long palpebral fissures persist, as does mild to moderate mental retardation. Independent daily living skills are achieved but a sheltered living environment is needed.

ICSI and the transmission of X-autosomal translocation: a three-generation evaluation of X;20 translocation: case report.

Published reports show that male carriers of an X-autosome translocation, which is either inherited from their mother or is de novo, are generally sterile, regardless of the position of the breakpoint in the X chromosome. We report a three-generation propagation of such a translocation in a family with a case of male factor infertility. Due to the condition of severe oligozoospermia, the proband and his wife underwent ICSI, which resulted in the birth of a normal healthy female. Cytogenetic (chromosome) analyses and X-chromosome inactivation (XCI) assays were done on the family. The cytogenetic analysis of the proband, a man with severe oligozoospermia, revealed an X-autosomal translocation, 46,Y,t(X;20)(q10;q10), which was inherited from his mother. His brother had the same translocation. Amniocentesis and post-natal umbilical cord analyses revealed that the female infant carried the same translocation as her father. XCI studies showed highly skewed inactivation of the normal X chromosome in the female infant, her paternal grandmother, and her mother who had a normal karyotype. In contrast to the data from the literature, our study suggests that men with a certain type of X-autosomal translocation could conceive children through ICSI in conditions in which a few spermatogonia are able to complete meiosis II. The literature involving X-autosomal translocation in males is also reviewed and the importance of the study of X-chromosomal inactivation in female infants discussed.