Targeted long-read sequencing identifies missing disease-causing variation.

Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.

Words matter: The language of difference in human genetics.

Diversity, equity, and inclusion efforts in academia are leading publishers and journals to re-examine their use of terminology for commonly used scientific variables. This reassessment of language is particularly important for human genetics, which is focused on identifying and explaining differences between individuals and populations. Recent guidance on the use of terms and symbols in clinical practice, research, and publications is beginning to acknowledge the ways that language and concepts of difference can be not only inaccurate but also harmful. To stop perpetuating historical wrongs, those of us who conduct and publish genetic research and provide genetic health care must understand the context of the terms we use and why some usages should be discontinued. In this article, we summarize critiques of terminology describing disability, sex, gender, race, ethnicity, and ancestry in research publications, laboratory reports, diagnostic codes, and pedigrees. We also highlight recommendations for alternative language that aims to make genetics more inclusive, rigorous, and ethically sound. Even though norms of acceptable language use are ever changing, it is the responsibility of genetics professionals to uncover biases ingrained in professional practice and training and to continually reassess the words we use to describe human difference because they cause harm to patients.

Practice resource-focused revision: Standardized pedigree nomenclature update centered on sex and gender inclusivity: A practice resource of the National Society of Genetic Counselors.

This focused revision builds on the expert opinions from the original publications of 'Recommendations for human standardized pedigree nomenclature' published in 1995 and updated in 2008. Our review of medical publications since 2008 did not identify any fundamental systematic alternative pedigree nomenclature. These findings attest to the relevance of most of the nomenclature with the critical exception of the nomenclature used to denote sex assigned at birth and gender. While we are not recommending the creation of any new pedigree symbols, a major focus of this publication is clarification of the use of symbols and language in the description of the distinction between sex and gender, with a view to ensuring safe and inclusive practice for people who are gender-diverse or transgender. In addition, we recommend modifications to the way that carrier status is depicted. Our goal is to respect individual differences and identities while maintaining biologically, clinically, and genetically meaningful information.

Taking an antiracist posture in scientific publications in human genetics and genomics.

From its earliest days, the field of human genetics has had a complex, and at times troubling, connection with racist ideologies. Although the modern field of human genetics and genomics has come a long way from those earlier errors, systemic racism remains ingrained in its institutions and practices. Although a variety of efforts are needed to excise systemic racism, we focus in this commentary on the work that must be done in scientific publishing in genetics and genomics. We propose eight principles that are both scientifically grounded and antiracist that we hope will serve as a foundation for the development of policies by publishers and editorial boards that address the unique needs of the field of genetics and genomics. Publishers and journals must go beyond mere policies, however. Editors and reviewers will need training on these policies and principles, and will benefit from resources like rubrics that can be used for evaluating the adherence of submissions to these guidelines.

Genetic counseling and screening of consanguineous couples and their offspring practice resource: Focused Revision.

There are no evidence-based guidelines to inform genetic counseling for consanguineous couples and their offspring. This focused revision builds on the expert opinions from the original publication of "Genetic Counseling and Screening of Consanguineous Couples and Their Offspring," based on a review of literature published since 2002.

Simultaneous germline and somatic sequencing in ovarian carcinoma: mutation rate and impact on clinical decision-making.

OBJECTIVE: Germline and somatic BRCA1 and BRCA2 (BRCA) mutations predict treatment response in patients with epithelial ovarian, peritoneal or fallopian tube cancer (OC), yet only germline testing is routinely pursued or reimbursed at diagnosis. We report our experience with clinical testing of paired tumor and germline DNA for OC mutations. METHODS: Simultaneous sequencing using the BROCA assay of DNA from paired blood and neoplastic tissue became clinically available at our institution in 2017. We retrospectively reviewed the medical records of OC cases tested from 7/2017 to 7/2018. We calculated the rates of known pathogenic germline mutations and actionable somatic mutations, defined as those for which targeted therapies exist. RESULTS: We identified 43 women (36 new diagnoses, seven recurrences) who underwent testing. Average age at diagnosis was 60. OC samples came from surgical specimens in 31 cases (72.1%), from biopsy in 11 cases (25.6%), and from cytology in one case (2.3%). We identified pathogenic germline mutations in six cases (14%), actionable somatic mutations in 15 cases (35%), and both a somatic and germline mutation in one case (2%). BRCA mutations accounted for 59% of all mutations. Of 40 cases with sufficient follow-up, providers documented reviewing results of genetic testing in 34 (85%), which influenced clinical decisions in 12 (30%). CONCLUSIONS: Simultaneous germline and tumor sequencing is an efficient way to provide enhanced information to guide the care of OC patients. This approach can identify somatic BRCA mutations at diagnosis, allowing physicians to provide PARP inhibitor maintenance and improve outcomes for those patients.

Assessing transgender and gender non-conforming pedigree nomenclature in current genetic counselors' practice: The case for geometric inclusivity.

Healthcare professionals rely on national organizations for guidance; the National Society of Genetic Counselors (NSGC) and the National Comprehensive Cancer Network (NCCN) have differing guidelines for acceptable pedigree symbols to represent transgender patients and minimal recommendations for gender non-conforming (GNC) patients. Inconsistency in accepted pedigree symbols to represent these patients is a barrier to providing them appropriate care. We assess variability in pedigree practice among genetic counselors and students, as well as reported education on serving the needs of the transgender and GNC communities, through a survey distributed through NSGC. Participants felt symbols similar to NSGC's (41.1%) and NCCN's (29.7%) recommendations for transgender patients are appropriate and emphasized a desire to affirm gender identity. We identified greater variability in symbols representing a GNC patient; 19.2% of participants selected 'other', explaining they were unsure of the appropriate choice. A high interest (99%) in further training demonstrates a recognition of education as an effective strategy for improving awareness and competency. Promotion of existing resources could help address the fact that 81% of participants were unaware of any standardized symbols used to represent transgender individuals. Creating affirming, standardized pedigree nomenclature is necessary for appropriate and consistent care.

Trends over 42 years in the Adult Medical Genetics Clinic at the University of Washington.

PURPOSE: We analyzed the patients served by the University of Washington Adult Genetic Medicine Clinic (UWAGMC) over a 42-year period to determine how clinical services have changed and to evaluate the contributing factors. METHODS: We conducted a retrospective survey of patients seen by UWAGMC that included patients seen from 1975 to 2016. Variables considered included referral indication, disease status, and clinic visit date. Indications for referral were then binned into clinical categories for descriptive analysis. RESULTS: Of 30,780 patient visits during the 39 years for which data were available, 57.3% occurred in the last decade. Referrals for breast/ovarian cancer or colon/endometrial cancer account for 74.8% of cancer referrals since 1998. Huntington disease patients made up 46% of neurological referral indications. Telephone screening implemented in 2013 has reduced the number of referrals for hypermobile Ehlers-Danlos syndrome. CONCLUSION: Referral indications increased with clinical testing availability and because of the academic programs of UWAGMC providers. With increased public awareness of heritable conditions, prescreening self-referrals were used to allocate limited resources. These trends demonstrate the need for more geneticists in adult medicine to expand centers of excellence for rare diseases and to serve the increasing numbers of adult patients with genetic conditions.

Insurance coverage does not predict outcomes of genetic testing: The search for meaning in payer decisions for germline cancer tests.

In this work, we explore the results of germline cancer genetic tests in individuals whose insurance would not cover this testing. We enrolled 31 patients with a personal history of cancer whose health insurer denied coverage for a clinical germline cancer panel genetic test recommended by a medical genetics provider into a study providing exome sequencing and return of cancer-related results. Five participants (16%) had a pathogenic variant identified related to increased cancer risk. Three participants (10%) had a variant of uncertain significance (VUS) in a gene related to their cancer history. These rates are not significantly different than the 12% rate of pathogenic or likely pathogenic (P/LP) variants and VUS in 1,462 patients approved by insurance to have a similar clinical germline cancer test (p = .59 for P/LP variants; p = .87 for VUS; Shirts et al., Genet Med, 18:974, 2016). Health insurance guidelines may not meaningfully differentiate between patients with cancer who are likely to benefit from germline cancer genetic testing and those who will not. Failure to identify pathogenic variants in this research cohort would have led to suboptimal care. Strategic evaluation of current germline cancer genetic testing coverage policies is needed to appropriately deliver precision medicine.

Rare loss of function variants in candidate genes and risk of colorectal cancer.

Although ~ 25% of colorectal cancer or polyp (CRC/P) cases show familial aggregation, current germline genetic testing identifies a causal genotype in the 16 major genes associated with high penetrance CRC/P in only 20% of these cases. As there are likely other genes underlying heritable CRC/P, we evaluated the association of variation at novel loci with CRC/P. We evaluated 158 a priori selected candidate genes by comparing the number of rare potentially disruptive variants (PDVs) found in 84 CRC/P cases without an identified CRC/P risk-associated variant and 2440 controls. We repeated this analysis using an additional 73 CRC/P cases. We also compared the frequency of PDVs in select genes among CRC/P cases with two publicly available data sets. We found a significant enrichment of PDVs in cases vs. controls: 20% of cases vs. 11.5% of controls with ≥ 1 PDV (OR = 1.9, p = 0.01) in the original set of cases. Among the second cohort of CRC/P cases, 18% had a PDV, significantly different from 11.5% (p = 0.02). Logistic regression, adjusting for ancestry and multiple testing, indicated association between CRC/P and PDVs in NTHL1 (p = 0.0001), BRCA2 (p = 0.01) and BRIP1 (p = 0.04). However, there was no significant difference in the frequency of PDVs at each of these genes between all 157 CRC/P cases and two publicly available data sets. These results suggest an increased presence of PDVs in CRC/P cases and support further investigation of the association of NTHL1, BRCA2 and BRIP1 variation with CRC/P.

National Society of Genetic Counselors Code of Ethics: Explication of 2017 Revisions.

The Code of Ethics (COE) of the National Society of Genetic Counselors (NSGC) was adopted in 1992 and was later revised and adopted in 2006. In 2016, the NSGC Code of Ethics Review Task Force (COERTF) was convened to review the COE. The COERTF reviewed ethical codes written by other professional organizations and suggested changes that would better reflect the current and evolving nature of the genetic counseling profession. The COERTF received input from the society's legal counsel, Board of Directors, and members-at-large. A revised COE was proposed to the membership and approved and adopted in April 2017. The revisions and rationale for each are presented.

Initiation of universal tumor screening for Lynch syndrome in colorectal cancer patients as a model for the implementation of genetic information into clinical oncology practice.

BACKGROUND: Lynch syndrome confers a hereditary predisposition to colorectal and other cancers. Universal tumor screening (UTS) for Lynch syndrome is recommended by several professional societies, but the implementation can be complex. This article describes the evaluation, process development, and initiation of Lynch syndrome UTS at a tertiary referral cancer center. METHODS: A multidisciplinary team developed the new process design. Issues in 5 themes were noted: timing, funding, second-opinion patients, result processing, and the role of genetics providers. A committee approach was used to examine each issue for process-improvement development. RESULTS: The issues related to testing were addressed individually for the successful implementation of UTS at the institutional level. In the conventional-care period, 9 of 30 cases (30%) received Lynch syndrome screening, and 4 cases were referred to medical genetics. During the 6 months following the implementation of UTS, 32 of 44 patients (73%) received Lynch syndrome screening. The 13 unscreened patients all had identified reasons for nonscreening (eg, financial limitations). Ten patients were referred to medical genetics, which identified no new cases of Lynch syndrome, but a low-risk adenomatous polyposis coli (APC) variant was detected in 1 individual. CONCLUSIONS: The implementation of effective Lynch syndrome UTS can feasibly alter practice at the institutional level. This experience with the assessment and management of issues relevant to the successful implementation of a new clinical care paradigm based on emerging technology has implications for the uptake of advances across molecular oncology into clinical practice, and this is highly relevant in the current era of rapidly evolving genomic technology.

Actionable, pathogenic incidental findings in 1,000 participants' exomes.

The incorporation of genomics into medicine is stimulating interest on the return of incidental findings (IFs) from exome and genome sequencing. However, no large-scale study has yet estimated the number of expected actionable findings per individual; therefore, we classified actionable pathogenic single-nucleotide variants in 500 European- and 500 African-descent participants randomly selected from the National Heart, Lung, and Blood Institute Exome Sequencing Project. The 1,000 individuals were screened for variants in 114 genes selected by an expert panel for their association with medically actionable genetic conditions possibly undiagnosed in adults. Among the 1,000 participants, 585 instances of 239 unique variants were identified as disease causing in the Human Gene Mutation Database (HGMD). The primary literature supporting the variants' pathogenicity was reviewed. Of the identified IFs, only 16 unique autosomal-dominant variants in 17 individuals were assessed to be pathogenic or likely pathogenic, and one participant had two pathogenic variants for an autosomal-recessive disease. Furthermore, one pathogenic and four likely pathogenic variants not listed as disease causing in HGMD were identified. These data can provide an estimate of the frequency (∼3.4% for European descent and ∼1.2% for African descent) of the high-penetrance actionable pathogenic or likely pathogenic variants in adults. The 23 participants with pathogenic or likely pathogenic variants were disproportionately of European (17) versus African (6) descent. The process of classifying these variants underscores the need for a more comprehensive and diverse centralized resource to provide curated information on pathogenicity for clinical use to minimize health disparities in genomic medicine.

Improving performance of multigene panels for genomic analysis of cancer predisposition.

PURPOSE: Screening multiple genes for inherited cancer predisposition expands opportunities for cancer prevention; however, reports of variants of uncertain significance (VUS) may limit clinical usefulness. We used an expert-driven approach, exploiting all available information, to evaluate multigene panels for inherited cancer predisposition in a clinical series that included multiple cancer types and complex family histories. METHODS: For 1,462 sequential patients referred for testing by BROCA or ColoSeq multigene panels, genomic DNA was sequenced and variants were interpreted by multiple experts using International Agency for Research on Cancer guidelines and incorporating evolutionary conservation, known and predicted variant consequences, and personal and family cancer history. Diagnostic yield was evaluated for various presenting conditions and family-history profiles. RESULTS: Of 1,462 patients, 12% carried damaging mutations in established cancer genes. Diagnostic yield varied by clinical presentation. Actionable results were identified for 13% of breast and colorectal cancer patients and for 4% of cancer-free subjects, based on their family histories of cancer. Incidental findings explaining cancer in neither the patient nor the family were present in 1.7% of subjects. Less than 1% of patients carried VUS in BRCA1 or BRCA2. For all genes combined, initial reports contained VUS for 10.5% of patients, which declined to 7.5% of patients after reclassification based on additional information. CONCLUSIONS: Individualized interpretation of gene panels is a complex medical activity. Interpretation by multiple experts in the context of personal and family histories maximizes actionable results and minimizes reports of VUS.Genet Med 18 10, 974-981.

Family Studies for Classification of Variants of Uncertain Classification: Current Laboratory Clinical Practice and a New Web-Based Educational Tool.

Multi-gene cancer panels often identify variants of uncertain clinical significance (VUS) that pose a challenge to health care providers in managing a patient's cancer risk. Family segregation analysis can yield powerful data to re-classify a VUS (as either benign or pathogenic). However, financial and personnel resources to coordinate these studies are limited. In an informal assessment we found that family studies for variant classification are done by most clinical genetics laboratories that offer hereditary cancer panel testing. The process for family studies differs substantially across laboratories. One near universal limitation is that families usually have too few individuals for an informative co-segregation analysis. A unique and potential resource-saving approach is to engage patients and their families in expanding their own pedigrees for segregation analysis of their VUS. We describe a novel public educational tool ( FindMyVariant.org ) designed to inform patients and genetic counselors about strategies to improve the probability of variant classification using familial segregation. While the web tool is designed to be useful for any gene, the project was primarily focused on VUS's returned in cancer risk genes. FindMyVariant.org is a resource for genetic providers to offer motivated families who are willing to gather information about their family relationships and history. Working alongside clinical or research genetic laboratories, the information they collect may help reclassify their VUS using segregation analysis.

Developing a Model of Advanced Training to Promote Career Advancement for Certified Genetic Counselors: An Investigation of Expanded Skills, Advanced Training Paths, and Professional Opportunities.

There are currently multiple paths through which genetic counselors can acquire advanced knowledge and skills. However, outside of continuing education opportunities, there are few formal training programs designed specifically for the advanced training of genetic counselors. In the genetic counseling profession, there is currently considerable debate about the paths that should be available to attain advanced skills, as well as the skills that might be needed for practice in the future. The Association of Genetic Counseling Program Directors (AGCPD) convened a national committee, the Committee on Advanced Training for Certified Genetic Counselors (CATCGC), to investigate varied paths to post-master's training and career development. The committee began its work by developing three related grids that view career advancement from the viewpoints of the skills needed to advance (skills), ways to obtain these skills (paths), and existing genetic counselor positions that offer career change or advancement (positions). Here we describe previous work related to genetic counselor career advancement, the charge of the CATCGC, our preliminary work in developing a model through which to view genetic counselor advanced training and career advancement opportunities, and our next steps in further developing and disseminating the model.

Next Generation Sequencing in the Clinic: a Patterns of Care Study in a Retrospective Cohort of Subjects Referred to a Genetic Medicine Clinic for Suspected Lynch Syndrome.

Next generation sequencing (NGS) gene panels are increasingly used in medical genetics clinics for the evaluation of common inherited cancer syndromes, but the clinical efficacy of these tests, and the factors driving clinical providers to order them are unclear. We conducted a patterns-of-care study to compare patients evaluated with NGS gene panels with a reference group. We abstracted demographic, socioeconomic, and clinical information in a retrospective cohort of patients referred to a large medical genetics clinic for evaluation of inherited colorectal cancer and polyposis syndromes. Patients tested with NGS gene panels were more likely to be insured compared to the reference group (85.3 % vs. 69.2 %, p = 0.0068),less likely to have prior tumor tissue testing (29.4 % vs. 54.3 %, p = 0.0004), and less likely to have an abnormal tumor tissue test result (46.7 % vs. 74.5 %, p = 0.01). No significant differences were found between groups in age, gender, race, employment status, personal history of colorectal cancer, or proportion of patients fulfilling Lynch syndrome clinical criteria. Patients with NGS testing were less likely to have a pathogenic/likely pathogenic variant detected (13.7 % vs. 31.9 %, p = 0.002). Patients referred for NGS testing to evaluate inherited colorectal cancer/polyposis risk appear to undergo tumor tissue testing less frequently than non-NGS testing patients. Further studies are needed to assess the most effective and cost-effective approach to genomic diagnosis in this patient population.

A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment.

DISCLAIMER: The practice guidelines of the American College of Medical Genetics and Genomics (ACMG) and the National Society of Genetic Counselors (NSGC) are developed by members of the ACMG and NSGC to assist medical geneticists, genetic counselors, and other health-care providers in making decisions about appropriate management of genetic concerns, including access to and/or delivery of services. Each practice guideline focuses on a clinical or practice-based issue and is the result of a review and analysis of current professional literature believed to be reliable. As such, information and recommendations within the ACMG and NSGC joint practice guidelines reflect the current scientific and clinical knowledge at the time of publication, are current only as of their publication date, and are subject to change without notice as advances emerge. In addition, variations in practice, which take into account the needs of the individual patient and the resources and limitations unique to the institution or type of practice, may warrant approaches, treatments, and/or procedures that differ from the recommendations outlined in this guideline. Therefore, these recommendations should not be construed as dictating an exclusive course of management, nor does the use of such recommendations guarantee a particular outcome. Genetic counseling practice guidelines are never intended to displace a health-care provider's best medical judgment based on the clinical circumstances of a particular patient or patient population. Practice guidelines are published by the ACMG or the NSGC for educational and informational purposes only, and neither the ACMG nor the NSGC "approve" or "endorse" any specific methods, practices, or sources of information.Cancer genetic consultation is an important aspect of the care of individuals at increased risk of a hereditary cancer syndrome. Yet several patient, clinician, and system-level barriers hinder identification of individuals appropriate for cancer genetics referral. Thus, the purpose of this practice guideline is to present a single set of comprehensive personal and family history criteria to facilitate identification and maximize appropriate referral of at-risk individuals for cancer genetic consultation. To develop this guideline, a literature search for hereditary cancer susceptibility syndromes was conducted using PubMed. In addition, GeneReviews and the National Comprehensive Cancer Network guidelines were reviewed when applicable. When conflicting guidelines were identified, the evidence was ranked as follows: position papers from national and professional organizations ranked highest, followed by consortium guidelines, and then peer-reviewed publications from single institutions. The criteria for cancer genetic consultation referral are provided in two formats: (i) tables that list the tumor type along with the criteria that, if met, would warrant a referral for a cancer genetic consultation and (ii) an alphabetical list of the syndromes, including a brief summary of each and the rationale for the referral criteria that were selected. Consider referral for a cancer genetic consultation if your patient or any of their first-degree relatives meet any of these referral criteria.

A mosaic PTEN mutation causing Cowden syndrome identified by deep sequencing.

PURPOSE: Mosaic PTEN mutations are not well described in Cowden syndrome. We report a 40-year-old woman with a clinical diagnosis of Cowden syndrome including Lhermitte-Duclos disease, who had a mosaic PTEN mutation detected by next-generation deep sequencing. METHODS: Complete PTEN gene sequencing by the Sanger method and deletion/duplication analysis performed on DNA extracted from blood leukocytes at a commercial clinical laboratory did not identify a mutation. Because of high suspicion of a PTEN mutation, we repeated testing by next-generation sequencing using the ColoSeq assay, which sequences the entire PTEN locus at >320-fold average coverage. RESULTS: ColoSeq identified a frameshift PTEN mutation (c.767_768delAG) in 1.7% of sequencing reads from peripheral blood leukocytes (21/1,184 reads), which is below the limit of detection of most Sanger sequencing methods. The mutation was detected at full heterozygous levels in skin fibroblasts and a cerebellar tumor, and at approximately the 25% level in colonic and endocervical mucosa, confirming somatic mosaicism. CONCLUSION: Our report highlights the power of deep next-generation sequencing to identify mosaic mutations that can be missed by traditional less sensitive approaches. We speculate that mosaic PTEN mutations are more common in Cowden syndrome than previously described.