Amy L. McGuire

The complete genome of an individual by massively parallel DNA sequencing.

The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of ‘genomic medicine’. However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2–40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of ‘personalized genome sequencing’.

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing

In clinical exome and genome sequencing, there is a potential for the recognition and reporting of incidental or secondary findings unrelated to the indication for ordering the sequencing but of medical value for patient care. The American College of Medical Genetics and Genomics (ACMG) recently published a policy statement on clinical sequencing that emphasized the importance of alerting the patient to the possibility of such results in pretest patient discussions, clinical testing, and reporting of results. The ACMG appointed a Working Group on Incidental Findings in Clinical Exome and Genome Sequencing to make recommendations about responsible management of incidental findings when patients undergo exome or genome sequencing. This Working Group conducted a year-long consensus process, including an open forum at the 2012 Annual Meeting and review by outside experts, and produced recommendations that have been approved by the ACMG Board. Specific and detailed recommendations, and the background and rationale for these recommendations, are described herein. The ACMG recommends that laboratories performing clinical sequencing seek and report mutations of the specified classes or types in the genes listed here. This evaluation and reporting should be performed for all clinical germline (constitutional) exome and genome sequencing, including the “normal” of tumor-normal subtractive analyses in all subjects, irrespective of age but excluding fetal samples. We recognize that there are insufficient data on penetrance and clinical utility to fully support these recommendations, and we encourage the creation of an ongoing process for updating these recommendations at least annually as further data are collected.Genet Med 2013:15(7):565–574

Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy

BACKGROUND Whole-genome sequencing may revolutionize medical diagnostics through rapid identification of alleles that cause disease. However, even in cases with simple patterns of inheritance and unambiguous diagnoses, the relationship between disease phenotypes and their corresponding genetic changes can be complicated. Comprehensive diagnostic assays must therefore identify all possible DNA changes in each haplotype and determine which are responsible for the underlying disorder. The high number of rare, heterogeneous mutations present in all humans and the paucity of known functional variants in more than 90% of annotated genes make this challenge particularly difficult. Thus, the identification of the molecular basis of a genetic disease by means of whole-genome sequencing has remained elusive. We therefore aimed to assess the usefulness of human whole-genome sequencing for genetic diagnosis in a patient with Charcot-Marie-Tooth disease. METHODS We identified a family with a recessive form of Charcot-Marie-Tooth disease for which the genetic basis had not been identified. We sequenced the whole genome of the proband, identified all potential functional variants in genes likely to be related to the disease, and genotyped these variants in the affected family members. RESULTS We identified and validated compound, heterozygous, causative alleles in SH3TC2 (the SH3 domain and tetratricopeptide repeats 2 gene), involving two mutations, in the proband and in family members affected by Charcot-Marie-Tooth disease. Separate subclinical phenotypes segregated independently with each of the two mutations; heterozygous mutations confer susceptibility to neuropathy, including the carpal tunnel syndrome. CONCLUSIONS As shown in this study of a family with Charcot-Marie-Tooth disease, whole-genome sequencing can identify clinically relevant variants and provide diagnostic information to inform the care of patients.

Identifying Personal Genomes by Surname Inference

Anonymity Compromised The balance between maintaining individual privacy and sharing genomic information for research purposes has been a topic of considerable controversy. Gymrek et al. (p. 321; see the Policy Forum by Rodriguez et al.) demonstrate that the anonymity of participants (and their families) can be compromised by analyzing Y-chromosome sequences from public genetic genealogy Web sites that contain (sometimes distant) relatives with the same surname. Short tandem repeats (STRs) on the Y chromosome of a target individual (whose sequence was freely available and identified in GenBank) were compared with information in public genealogy Web sites to determine the shortest time to the most recent common ancestor and find the most likely surname, which, when combined with age and state of residency identified the individual. When STRs from 911 individuals were used as the starting points, the analysis projected a success rate of 12% within the U.S. male population with Caucasian ancestry. Further analysis of detailed pedigrees from one collection revealed that families of individuals whose genomes are in public repositories could be identified with high probability. Anonymity of male personal genome data sets can be compromised by means of publicly available data. [Also see News story and Policy Forum by Rodriguez et al.] Sharing sequencing data sets without identifiers has become a common practice in genomics. Here, we report that surnames can be recovered from personal genomes by profiling short tandem repeats on the Y chromosome (Y-STRs) and querying recreational genetic genealogy databases. We show that a combination of a surname with other types of metadata, such as age and state, can be used to triangulate the identity of the target. A key feature of this technique is that it entirely relies on free, publicly accessible Internet resources. We quantitatively analyze the probability of identification for U.S. males. We further demonstrate the feasibility of this technique by tracing back with high probability the identities of multiple participants in public sequencing projects.

An Unwelcome Side Effect of Direct-to-Consumer Personal Genome Testing: Raiding the Medical Commons

It is now possible for individuals to learn about their genetic susceptibility to dozens of common and complex disorders, such as coronary artery disease, diabetes, obesity, prostate cancer, and Alzheimer’s disease, without ever seeing a physician. Direct-to-consumer personal genome testing companies, such as 23andMe, Navigenics, and deCODEme hope to empower consumers to take control of their health by providing tailored assessments of genetic risk based on reported associations between genomic variation and susceptibility to disease. Several states limit or forbid this practice as a violation of state law that requires the appropriate involvement of a licensed physician when providing medical diagnostic information (1). Personal genome testing companies claim that their services are for informational and educational purposes only. They warn consumers that the information should not be used for diagnosis, treatment, or health ascertainment purposes and direct them to their physician if they have questions or concerns about their health status (2–3). Because of uncertainty about the validity and clinical utility of test results, Hunter and colleagues advise physicians to discourage patients from pursuing personal genome testing and to respond to test results with general statements about their limited predictive value (4). While this response is consistent with current knowledge, a recent survey of online social networking users suggests that at least some potential consumers would expect their physician to help them interpret test results and believe that physicians have a professional obligation to do so (ALM, unpublished data). This expectation has important implications for primary care physicians, even pediatricians, because many direct-to-consumer personal genome testing companies allow testing of children as well as adults. Primary care physicians already spend much of their time helping patients understand and manage health risks. Assessment of cardiac risk factors, occupational exposures and other health indicators allow physicians to identify health risks and counsel patients accordingly. Physicians are also accustomed to talking with patients about health information disclosed on the internet or through other media outlets. At the same time, primary care physicians have limited time with patients, face many competing demands (5), and are poorly reimbursed for time spent counseling patients about preventive care. Patient concerns about direct-to-consumer test results have the potential to exacerbate these problems and strain already limited health care resources.

Ethical and Practical Guidelines for Reporting Genetic Research Results to Study Participants: Updated Guidelines From a National Heart, Lung, and Blood Institute Working Group

In January 2009, the National Heart, Lung, and Blood Institute convened a 28-member multidisciplinary Working Group to update the recommendations of a 2004 National Heart, Lung, and Blood Institute Working Group focused on Guidelines to the Return of Genetic Research Results. Changes in the genetic and societal landscape over the intervening 5 years raise multiple questions and challenges. The group noted the complex issues arising from the fact that technological and bioinformatic progress has made it possible to obtain considerable information on individuals that would not have been possible a decade ago. Although unable to reach consensus on a number of issues, the working group produced 5 recommendations. The working group offers 2 recommendations addressing the criteria necessary to determine when genetic results should and may be returned to study participants, respectively. In addition, it suggests that a time limit be established to limit the duration of obligation of investigators to return genetic research results. The group recommends the creation of a central body, or bodies, to provide guidance on when genetic research results are associated with sufficient risk and have established clinical utility to justify their return to study participants. The final recommendation urges investigators to engage the broader community when dealing with identifiable communities to advise them on the return of aggregate and individual research results. Creation of an entity charged to provide guidance to institutional review boards, investigators, research institutions, and research sponsors would provide rigorous review of available data, promote standardization of study policies regarding return of genetic research results, and enable investigators and study participants to clarify and share expectations for the handling of this increasingly valuable information with appropriate respect for the rights and needs of participants.

Research Ethics Recommendations for Whole-Genome Research: Consensus Statement

Interest in whole-genome research has grown substantially over the past few months. This article explores the challenging ethics issues associated with this work.

Exploring concordance and discordance for return of incidental findings from clinical sequencing

Purpose:The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing.Methods:Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted in silico to be pathogenic.Results:On average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes.Conclusion:Specialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing.Genet Med 2012:14(4):405–410

Ethics and Genomic Incidental Findings

Laboratories have an obligation to report clinically beneficial incidental findings. The American College of Medical Genetics and Genomics (ACMG) recently issued a statement (1) recommending that all laboratories conducting clinical sequencing seek and report pathogenic and expected pathogenic mutations for a short list of carefully chosen genes and conditions. The recommendations establish a baseline for reporting clinically relevant incidental findings and articulate ethical principles relevant to their disclosure. The ACMG acknowledged that the list will evolve over time and is developing a mechanism for community input (2). This paper focuses on the ethical framework for the recommendations, rather than on the choice of which genes to include on the list.

Personalized genomic information: preparing for the future of genetic medicine

The falling cost of sequencing means that we are rapidly approaching an era in which access to personalized genomic information is likely to be widespread. Here, four experts with different insights into the field of genomic medicine answer questions about the prospects for using this type of information. Their responses highlight the diverse range of issues that must be addressed — ranging from scientific to ethical and logistical — to ensure that the potential benefits of personal genomic information outweigh the costs to both individuals and societies.