Anna Middleton

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

Summary Background Human genome sequencing has transformed our understanding of genomic variation and its relevance to health and disease, and is now starting to enter clinical practice for the diagnosis of rare diseases. The question of whether and how some categories of genomic findings should be shared with individual research participants is currently a topic of international debate, and development of robust analytical workflows to identify and communicate clinically relevant variants is paramount. Methods The Deciphering Developmental Disorders (DDD) study has developed a UK-wide patient recruitment network involving over 180 clinicians across all 24 regional genetics services, and has performed genome-wide microarray and whole exome sequencing on children with undiagnosed developmental disorders and their parents. After data analysis, pertinent genomic variants were returned to individual research participants via their local clinical genetics team. Findings Around 80 000 genomic variants were identified from exome sequencing and microarray analysis in each individual, of which on average 400 were rare and predicted to be protein altering. By focusing only on de novo and segregating variants in known developmental disorder genes, we achieved a diagnostic yield of 27% among 1133 previously investigated yet undiagnosed children with developmental disorders, whilst minimising incidental findings. In families with developmentally normal parents, whole exome sequencing of the child and both parents resulted in a 10-fold reduction in the number of potential causal variants that needed clinical evaluation compared to sequencing only the child. Most diagnostic variants identified in known genes were novel and not present in current databases of known disease variation. Interpretation Implementation of a robust translational genomics workflow is achievable within a large-scale rare disease research study to allow feedback of potentially diagnostic findings to clinicians and research participants. Systematic recording of relevant clinical data, curation of a gene–phenotype knowledge base, and development of clinical decision support software are needed in addition to automated exclusion of almost all variants, which is crucial for scalable prioritisation and review of possible diagnostic variants. However, the resource requirements of development and maintenance of a clinical reporting system within a research setting are substantial. Funding Health Innovation Challenge Fund, a parallel funding partnership between the Wellcome Trust and the UK Department of Health.

Prenatal Diagnosis for Inherited Deafness—What is the Potential Demand?

Genetic testing for inherited deafness is now available within some genetics centres. This study used a structured questionnaire to assess the potential uptake of prenatal diagnosis (PND) for inherited deafness, and document the opinions of deaf and hearing individuals toward PND and termination of pregnancy (TOP) for hearing status. Participants were self-selected from the whole of the UK, of whom 644 were deaf, 143 were hard of hearing or deafened, and 527 were hearing individuals who had either a deaf parent or child. The results showed that 21% of deaf, 39% of hard of hearing and deafened, and 49% of hearing participants said they would consider PND for deafness. Six percent of deaf, 11% of hard of hearing and deafened, and 16% of hearing participants said they would consider a TOP if the fetus was found to be deaf. Two percent of deaf participants said they would prefer to have deaf children and would consider a TOP if the fetus was found to be hearing.

Congenital non-syndromal sensorineural hearing impairment due to connexin 26 gene mutations — molecular and audiological findings

We screened DNA from 72 sibships and 138 sporadically affected individuals with congenital non-syndromal sensorineural hearing impairment (NSSNHI) for mutations in the 26 (CX26) gene. A total of 20 (27.8%) of the sibships and 11 (7.9%) of the sporadically affected individuals were homozygous or compound heterozygotes for CX26 mutations. A total of 11 (17.2%) of 64 individuals with severe and 30 (30%) of 100 with profound NSSNHI compared to eight (8.7%) of 92 persons with moderate and none (0%) of 19 individuals with mild hearing impairment were homozygous or compound heterozygotes for CX26 mutations (chi2 test, 3 df, P = 0.000). CX26 mutation status bad no effect on the symmetry of the hearing impairment or configuration of the audiogram. In addition, serial audiograms showed no evidence of progression of the hearing impairment or differences in the severity of the hearing impairment in affected siblings in persons whether or not due to CX26 mutations. Sporadically affected individuals with congenital NSSNHI should be routinely tested for mutations in CX26, especially if the hearing impairment is severe or profound in severity, since identification of a mutation in CX26 allows use of Mendelian recurrence risks.

Policy challenges of clinical genome sequencing

Around the world, genome sequencing is moving from research into the clinic, and in the UK plans to sequence the genomes of 100 000 NHS patients are well underway. A clear policy on how to conduct genomic testing is therefore both essential and urgent, argue Caroline Wright and colleagues

Preferences for communication in clinic from deaf people: a cross-sectional study

AIMS AND OBJECTIVES To explore the preferences of deaf people for communication in a hospital consultation. METHODS Design--cross-sectional survey, using a structured, postal questionnaire. Setting--survey of readers of two journals for deaf and hard of hearing people. Participants--999 self-selected individuals with hearing loss in the UK, including those who use sign language and those who use speech. Main outcome measures--preferred mode of communication. RESULTS A total of 11% of participants preferred to use sign language within everyday life, 70% used speech and 17% used a mixture of sign and speech. Within a clinic setting, 50% of the sign language users preferred to have a consultation via a sign language interpreter and 43% indicated they would prefer to only have a consultation directly with a signing health professional; 7% would accept a consultation in speech as long as there was good deaf awareness from the health professional, indicated by a knowledge of lip-reading/speech-reading. Of the deaf speech users, 98% preferred to have a consultation in speech and of this group 71% indicated that they would only accept this if the health professional had good deaf awareness. Among the participants who used a mixture of sign language and speech, only 5% said they could cope with a consultation in speech with no deaf awareness whereas 46% were accepting of a spoken consultation as long as it was provided with good deaf awareness; 30% preferred to use an interpreter and 14% preferred to have a consultation directly with a signing health professional. CONCLUSIONS The hospital communication preferences for most people with deafness could be met by increasing deaf awareness training for health professionals, a greater provision of specialized sign language interpreters and of health professionals who can use fluent sign language directly with clients in areas where contact with deaf people is frequent.

No expectation to share incidental findings in genomic research

Genomic sequencing studies can answer questions about the genetic contribution to complex medical disorders such as developmental disorders. Although fi ndings relating to the disorder of interest will be communicated to patients along with appropriate counselling, there is pressure on researchers to return secondary or incidental findings (ie, additional health-related data unrelated to the research question). But few studies have actually asked relevant stakeholders what their expectations are of researchers. Analysing and returning extensive data from genetic studies poses a particular dilemma simply because of the scale—with potentially hundreds of relevant variants that could be linked to future medical health. For many researchers, an exploration of such variants would have implications for time and resources that could compromise the ability to do research. Incidental findings could be uncovered by accident while exploring a pertinent finding, or might be revealed through a deliberate search for particular genes linked, for example, to serious, life-threatening treatable disorders. Whether to do such an opportunistic screen and what to do with incidental, health-related data, is subject to debate. With an online survey containing ten explanatory films, we gathered the attitudes of 6944 people from 75 different countries towards their expectations of genomic researchers with respect to sharing incidental fi ndings. These participants included four relevant stakeholder groups in sequencing research: members of the public (n=4961), genomic researchers (n=607), genetic health professionals (n=533), and other health professionals (eg, nurses, surgeons, paediatricians, and general physicians; n=843). We asked participants whether incidental findings from genome studies should be made available to research participants; and whether they expected researchers to deliberately do an opportunistic screen to look for incidental fi ndings of particular health relevance. 5628 of 6370 respondees thought that incidental findings should be made available to research participants (fi gure). However, despite such a strong interest in having access to data, only 1741 of 5653 participants expected genomic researchers to actively search for incidental fi ndings not relevant to their research. These results remained consistent even after adjustment for potential confounding eff ects. When asked, stakeholders do not expect researchers to search actively for incidental fi ndings in a research setting. The US Presidential Commission for the Study of Bioethical Issues also suggests that researchers do not have a duty to actively look for incidental fi ndings. Although researchers might choose to explore and share incidental fi ndings, within an appropriate ethics framework, our survey supports a policy that does not obligate researchers to search for and then communicate incidental findings to research participants.

Position statement on opportunistic genomic screening from the Association of Genetic Nurses and Counsellors (UK and Ireland)

The American College of Medical Genetics and Genomics released recommendations for reporting incidental findings (IFs) in clinical exome and genome sequencing. These suggest ‘opportunistic genomic screening’ should be available to both adults and children each time a sequence is done and would be undertaken without seeking preferences from the patient first. Should opportunistic genomic screening be implemented in the United Kingdom, the Association of Genetic Nurses and Counsellors (AGNC), which represents British and Irish genetic counsellors and nurses, feels strongly that the following must be considered (see article for complete list): (1) Following appropriate genetic counselling, patients should be allowed to consent to or opt out of opportunistic genomic screening. (2) If true IFs are discovered the AGNC are guided by the report from the Joint Committee on Medical Genetics about the sharing of genetic testing results. (3) Children should not be routinely tested for adult-onset conditions. (4) The formation of a list of variants should involve a representative from the AGNC as well as a patient support group. (5) The variants should be for serious or life-threatening conditions for which there are treatments or preventative strategies available. (6) There needs to be robust evidence that the benefits of opportunistic screening outweigh the potential harms. (7) The clinical validity and utility of variants should be known. (8) There must be a quality assurance framework that operates to International standards for laboratory testing. (9) Psychosocial research is urgently needed in this area to understand the impact on patients.

Report from the UK and Eire Association of Genetic Nurses and Counsellors (AGNC) Supervision Working Group on Genetic Counselling Supervision

The Association of Genetic Nurses and Counsellors (AGNC) is the professional organisation which represents genetic counsellors and genetic nurses in the United Kingdom (UK) and Eire. The AGNC recognises that genetic counselling supervision is instrumental to the practice, training and registration of genetic counsellors in the UK. The AGNC formed a Supervision Working Group, whose terms of reference were to collate information on supervision and create a list of ‘best practice’ recommendations for its genetic counsellor members. This report delivers the findings from the Supervision Working Group and has been peer reviewed by the AGNC membership in the UK and Eire and ratified by the AGNC Committee. It offers a working definition of genetic counselling supervision, gives an overview of some of the literature on supervision and concludes with practice recommendations.

Potential research participants support the return of raw sequence data

Health-related results that are discovered in the process of genomic research should only be returned to research participants after being clinically validated and then delivered and followed up within a health service. Returning such results may be difficult for genomic researchers who are limited by resources or unable to access appropriate clinicians. Raw sequence data could, in theory, be returned instead. This might appear nonsensical as, on its own, it is a meaningless code with no clinical value. Yet, as and when direct to consumer genomics services become more widely available (and can be endorsed by independent health professionals and genomic researchers alike), the return of such data could become a realistic proposition. We explore attitudes from <7000 members of the public, genomic researchers, genetic health professionals and non-genetic health professionals and ask participants to suggest what they would do with a raw sequence, if offered it. Results show 62% participants were interested in using it to seek out their own clinical interpretation. Whilst we do not propose that raw sequence data should be returned at the moment, we suggest that should this become feasible in the future, participants of sequencing studies may possibly support this.

Empirical research on the ethics of genomic research

© 2013 Wiley Periodicals, Inc.