Karin M. Dent

Exome sequencing identifies the cause of a mendelian disorder

We demonstrate the first successful application of exome sequencing to discover the gene for a rare mendelian disorder of unknown cause, Miller syndrome (MIM%263750). For four affected individuals in three independent kindreds, we captured and sequenced coding regions to a mean coverage of 40× and sufficient depth to call variants at ∼97% of each targeted exome. Filtering against public SNP databases and eight HapMap exomes for genes with two previously unknown variants in each of the four individuals identified a single candidate gene, DHODH, which encodes a key enzyme in the pyrimidine de novo biosynthesis pathway. Sanger sequencing confirmed the presence of DHODH mutations in three additional families with Miller syndrome. Exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits.

Improved molecular diagnosis of dystrophinopathies in an unselected clinical cohort.

Mutations in the DMD gene result in Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD). Readily available clinical tests detect only deletions of one exon or greater, which are found in approximately 60% of cases. Mutational analysis of other types of DMD mutations, such as premature stop codons and small frameshifting insertions or deletions, has historically been hampered by the large size of the gene. We have recently reported a method that allows the rapid and economical sequencing of the entire coding region of the DMD gene, and that is more sensitive than methods based on single‐strand conformational polymorphism (SSCP) screening or other preliminary screening steps. Here we use single condition amplification/internal primer (SCAIP) sequencing analysis, in combination with multiplex amplifiable probe hybridization (MAPH) analysis of duplications, to report the frequency of mutations in a large cohort of unselected dystrophinopathy patients from a single clinic. Our results indicate that 7% of dystrophinopathy patients do not have coding region mutations, suggesting that intronic mutations are not uncommon. The availability of rapid and thorough mutation analysis from peripheral blood samples, along with an improved estimate of the percentage of non‐coding region mutations, will be of benefit for improved genetic counseling and in identification of cohorts for clinical trials.

Informed consent for whole genome sequencing: a qualitative analysis of participant expectations and perceptions of risks, benefits, and harms.

Scientific evidence on the extent to which ethical concerns about privacy, confidentiality, and return of results for whole genome sequencing (WGS) are effectively conveyed by informed consent (IC) is lacking. The aim of this study was to learn, via qualitative interviews, about participant expectations and perceptions of risks, benefits, and harms of WGS. Participants in two families with Miller syndrome consented for WGS were interviewed about their experiences of the IC process and their perceptions of risks, benefits, and harms of WGS. Interviews were transcribed and analyzed for common themes. IC documents are included in the Supplementary Materials. Participants expressed minimal concerns about privacy and confidentiality with regard to both their participation and sharing of their WGS data in restricted access databases. Participants expressed strong preferences about how results should be returned, requesting both flexibility of the results return process and options for the types of results to be returned. Participant concerns about risks to privacy and confidentiality from broad sharing of WGS data are likely to be strongly influenced by social and medical context. In these families with a rare Mendelian syndrome, the perceived benefits of participation strongly trumped concerns about risks. Individual preferences, for results return, even within a family, varied widely. This underscores the need to develop a framework for results return that allows explicitly for participant preferences and enables modifications to preferences over time. Web‐based tools that facilitate participant management of their individual research results could accommodate such a framework.

Practices and Policies of Clinical Exome Sequencing Providers: Analysis and Implications

Exome and whole genome sequencing (ES/WGS) offer potential advantages over traditional approaches to diagnostic genetic testing. Consequently, use of ES/WGS in clinical settings is rapidly becoming commonplace. Yet there are myriad moral, ethical, and perhaps legal implications attached to the use of ES and health care professionals and institutions will need to consider these implications in the context of the varied practices and policies of ES service providers. We developed “core elements” of content and procedures for informed consent, data sharing, and results management and a quantitative scale to assess the extent to which research protocols met the standards established by these core elements. We then used these tools to evaluate the practices and policies of each of the 6 U.S. CLIA‐certified labs offering clinical ES. Approaches toward informed consent, data sharing, and results return vary widely among ES providers as do the overall potential merits and disadvantages of each, and more importantly, the balance between the two.

Methodology of a multistate study of congenital hearing loss: Preliminary data from Utah newborn screening

A multistate Centers for Disease Control and Prevention (CDC) study was designed to investigate the etiology of congenital hearing loss in infants ascertained through state‐mandated hearing screening or early hearing loss detection and intervention (EHDI) programs. At least 50% of permanent childhood‐onset hearing loss is due to genetic causes, and approximately 20% of all infants with congenital hearing loss have mutations in the GJB2 gene. Another 1% of childhood hearing loss is due to mitochondrial DNA (mtDNA) mutations. The specific aims of this study are to 1) classify the etiology of congenital hearing loss in infants by doing prospective genetic evaluations of all newborns with permanent hearing loss from defined geographic areas, 2) determine the frequency of mutations in GJB2 and two common mitochondrial mutations in these populations, and 3) establish a model infrastructure linking genetic services to statewide EHDI programs. As of April 2003, Utah is the only center evaluating patients. Study subjects identified through the Utah Department of Health EHDI program are contacted by letter and offered a comprehensive medical genetics evaluation with DNA testing for GJB2 and mitochondrial mutations A1555G and A7445G. To date, 25 probands and their immediate family members have been evaluated. We have identified 20 cases with nonsyndromic hearing loss (7 multiplex and 13 simplex), 4 with syndromic hearing loss, and 1 with presumed cytomegalovirus (CMV)‐induced hearing loss. Six of 19 (32%) nonsyndromic cases with sensorineural hearing loss have mutations of one or both alleles of the GJB2 gene, and 21% are homozygous or compound heterozygotes for the 35delG mutation. No A1555G or A7445G mtDNA mutations have been found. Data reported to date include only children born in Utah, but EHDI programs in Hawaii, Rhode Island, and designated areas of Georgia have begun enrolling children in what is now a multistate collaborative study. This is the first comprehensive investigation to determine the etiology of hearing loss from populations ascertained through EHDI programs. The results of this study will facilitate the incorporation of genetic services into EHDI programs.

6q subtelomeric deletion: is there a recognizable syndrome?

We report on a girl with an abnormal hybridization pattern for the subtelomeric fluorescence in-situ hybridization (FISH) probe panel showing deletion of the long arm telomeric region of chromosome 6. All other subtelomere DNA probes showed normal hybridization patterns. Metaphase cells analysed from cultures of peripheral blood revealed a normal female chromosome complement at the 650-band level. The deletion was further characterized using genomic microarray analysis. Clinical findings include: developmental delay, seizures, hypoplasia of the corpus callosum, dextrocardia, unusual dimpling of knees and elbows, and minor anomalies. We are aware of only two other reports of isolated cryptic 6q subtelomeric deletions not associated with other chromosomal abnormalities. The absence of retinal abnormalities in our case supports the theory that genes responsible for the retinal abnormalities in other terminal 6q deletions are proximal to 6q27. Subtelomeric FISH probes were useful in establishing a diagnosis in our patient. As more cases are reported, we may be able to establish discrete phenotypes and natural histories that can aid in counselling families.

Ethical issues in cancer genetics: I 1) whose information is it?

This article presents and discusses four clinical cases that exemplify the complexity of ethical dilemmas concerning the provider’s obligation to disclose or withhold genetic information from patients.Case 1: What is the responsibility of the cancer genetics provider to ensure that a positive test results is shared with distant relatives?Case 2: To ensure that results go to at-risk relatives, do we have the right to ignore the wishes of the designated next-of-kin?Case 3: Do we have the right to reveal a familial BRCA1 mutation to a patient’s relative, who is at 50% risk?Case 4: Do we have an obligation to reveal that a patient is not a blood relative and therefore, not at risk to have inherited a familial mutation?These cases form the basis for discussing the provider’s dual obligations to keeping patient confidentiality and informing patients and families about risk (i.e. duty to warn). We also provide a summary of consensus points and additional discussion questions for each case.

My46: a Web-based tool for self-guided management of genomic test results in research and clinical settings.

A major challenge to implementing precision medicine is the need for an efficient and cost-effective strategy for returning individual genomic test results that is easily scalable and can be incorporated into multiple models of clinical practice. My46 is a Web-based tool for managing the return of genetic results that was designed and developed to support a wide range of approaches to disclosing results, ranging from traditional face-to-face disclosure to self-guided models. My46 has five key functions: set and modify results-return preferences, return results, educate, manage the return of results, and assess the return of results. These key functions are supported by six distinct modules and a suite of features that enhance the user experience, ease site navigation, facilitate knowledge sharing, and enable results-return tracking. My46 is a potentially effective solution for returning results and supports current trends toward shared decision making between patients and providers and patient-driven health management.Genet Med 19 4, 467–475.

Stress and coping in parents of children with Prader-Willi syndrome: Assessment of the impact of a structured plan of care

Hyperphagia, developmental delays, and maladaptive behaviors are common in Prader‐Willi syndrome (PWS) likely resulting in heightened parental stress. Objectives were to evaluate stress, describe usefulness of coping behaviors, and assess the impact of a structured Plan of Care (PC) on parents with children with PWS. Parents answered Perceived Stress Scale (PSS‐14), Coping Health Inventory for Parents (CHIP), and narrative/demographic surveys. The PC was introduced to a cohort of parents after completion of the PSS‐14 and CHIP and re‐administered 4–6 month after the introduction of the PC. Higher parental stress (n = 57) was observed compared to the general population, and associated with parents age, number of children living at home, and childs age and residential setting. “Maintaining family integration, cooperation, and an optimistic definition of the situation” was the most useful coping pattern. Thirty‐eight parents answered the PSS‐14 and CHIP after the PC. Parental stress decreased after the PC (P = 0.035). Coping behaviors related to “maintaining family integration” increased after the PC (P = 0.042). Women and men preferred different coping patterns before and after the PC. In conclusion, parental stress is increased in PWS, and a PC decreased stress and increased coping behaviors related to family stability for parents with children with PWS.

Goltz syndrome and PORCN mosaicism

Goltz syndrome, also known as focal dermal hypoplasia, is characterized primarily by ectodermal and mesodermal defects. Manifestations include cutis aplasia, dermal hypoplasia, papillomas, chorioretinal colobomas, absent/dysplastic teeth, and skeletal anomalies. Goltz syndrome is an X‐linked disorder due to mutations in PORCN, with a predominance of females affected. Germline mutations in PORCN are thought to result in embryonically lethality in males. We present a boy with a phenotype consistent with Goltz syndrome with low‐level mosaicism for a novel mutation in PORCN from peripheral blood (c.956dupA; p.Asn320GlufsX99).