Identification of Medically Actionable Secondary Findings in the 1000 Genomes

The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.     

Training for excellence in the inner city: an interview with Richard Savage and Clare Vaughan. Interview by Douglas Carnall.

Recruitment to general practice is at its lowest level for 30 years, and many vocational training schemes report difficulty in attracting new trainees. Spurred on by the aging population of south London, and with the advantage of pounds 1.3m of development money resulting from the Tomlinson report, the south London organisation of vocational training schemes (SLOVTS) has perhaps been able to cope better than most. Its chair, Richard Savage, a general practitioner and course organiser, and Clare Vaughan, an assistant adviser, have devised and implemented many innovative training posts for general practice over the past two years, and their approach seems to be bearing fruit: most of the doctors who have finished the training scheme are now entering practice in south London. They talked to Douglas Carnall about the causes of the crisis and the measures they have implemented to counter it. Clare Vaughan died in the week following the interview (see obituary, p 555).     

Early-replication DNA patterns in a derivative chromosome in a syrian hamster with only 42 chromosomes

From crosses within a 2n = 43 line of Syrian hamsters (Mesocricetus auratus) lacking one derivative (der 11) of an 11;20 reciprocal translocation we have obtained homozygotes with only 42 chromosomes These animals are homozygous deficient (nullisomic) for the centromere and short arm of chromosome 11 and for the bulk of the long arm of chromosome 20. — During cytogenetic studies, we investigated the frequency patterns of early-replicating bands in the surviving derivative (der 20) at two cytologically defined sub-phases of S using short-term fibroblast cultures. These patterns were compared with those observed in the component, untranslocated arms in normal 2n = 44 cells at the same two sub-phases. — Very close agreement was found, indicating that neither the nullisomy, nor the new arm combination has interfered detectably with the pattern or programme of early band replication.     

The endocrinology of puberty and reproductive functioning in female cotton-top tamarins (Saguinus oedipus) under varying social conditions

Sexual maturation and fertility were assessed in fourteen cotton-top tamarin (Saguinus oedipus) females under various social conditions. Six tamarin females (20-28 mo of age) showed a suppression of fertility while living with their families. Hormonal profiles demonstrated low, acyclic levels of urinary luteinizing hormone (LH) and estrone-conjugates (E1C). A rapid onset of ovarian and pituitary cyclicity occurred when four of the six females were removed from their families and paired with an unrelated male. In one female, an ovulatory LH peak occurred as early as eight days after pairing and resulted in conception and full-term pregnancy. Two of the six females were housed in total isolation for 30 days following their removal from the family and prior to pairing. Gradual increases in hormone concentrations occurred during isolation; however, there was no ovarian cyclicity until each female was paired with an unrelated male. In all six females, conception occurred before or as a result of the third ovulatory cycle. Partial isolation of a 36-mo-old female resulted in elevated LH and E1C levels, but cyclicity was not observed until the female was paired with an unrelated male. These findings indicate that removal of a female from the family alone does not initiate ovarian cycling. Sexual maturation, or puberty, occurs in female tamarins living with their families between 15 and 17 mo of age when mean LH and E1C levels began to increase. However, when a female is removed and paired at 9 mo of age with an unrelated male, elevated levels of LH and E1C may be seen by 10 and 11 mo of age. Our findings indicate that a suppression of fertility occurs in cotton-top tamarins living with their families, but that reproductive suppression does not affect the process of sexual maturation. Both removal from the family environment and stimulation by an unrelated male tamarin were necessary to induce normal reproductive activity. An acceleration of puberty occurred when a female tamarin was removed from her family early in development and paired with a male.