Whole-genome sequencing in health care: recommendations of the European Society of Human Genetics. Eur J Hum Genet. 2013;21:580-584. [PMID: 23676617 DOI: 10.1038/ejhg.2013.46]

An ESHG-ESHRE survey on the current practice of expanded carrier screening in medically assisted reproduction

STUDY QUESTION

What is the current practice and views on (expanded) carrier screening ((E)CS) among healthcare professionals in medically assisted reproductive (MAR) practices in Europe?

SUMMARY ANSWER

The findings show a limited support for ECS with less than half of the respondents affiliated to centres offering ECS, and substantial variation in practice between centres in Europe.

WHAT IS KNOWN ALREADY

The availability of next-generation sequencing, which enables testing for large groups of genes simultaneously, has facilitated the introduction and expansion of ECS strategies, currently offered particularly in the private sector in the context of assisted reproduction.

STUDY DESIGN, SIZE, DURATION

A cross-sectional survey evaluating practice and current views among professionals working in MAR practice in different European countries was designed using the online SurveyMonkey tool. The web-based questionnaire included questions on general information regarding the current practice of (E)CS in MAR and questions on what is offered, to whom the test is offered, and how it is offered. It consisted mostly of multiple-choice questions with comment boxes, but also included open questions on the respondents' attitudes/concerns relevant to (E)CS practice, and room to upload requested files (e.g. guidelines and gene panels). In total, 338 responses were collected from 8 February 2022 to 11 April 2022.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The online survey was launched with an invitation email from the ESHRE central office (n = 4889 emails delivered) and the European Society of Human Genetics (ESHG) central office (n = 1790 emails delivered) sent to the ESHRE and ESHG members, and by social media posts. The survey was addressed to European MAR centres or gamete banks and to centres located in non-European countries participating in the European IVF-monitoring Consortium. Two reminder emails were sent. After exclusion of 39 incomplete responses received (e.g. only background information), 299 respondents from 40 different countries were included for analyses.

MAIN RESULTS AND THE ROLE OF CHANCE

Overall, 42.5% (127/299) of respondents were affiliated to centres offering ECS. The perceived responsibility to enable prospective parents to make informed reproductive decisions and preventing suffering/burden for parents were the main reasons to offer ECS. A single ECS panel is offered by nearly 45% (39/87 received answers) of the centres offering ECS, 25.3% (22/87) of those centres offer a selection of ECS panels, and 29.9% (26/87) offer whole exome sequencing and a large in silico panel. Different ranges of panel sizes and conditions were included in the ECS panel(s) offered. Most of the respondents (81.8%; 72/88 received answers) indicated that the panels they offer are universal and target the entire population. Pathogenic variants (89.7%; 70/78 received answers), and to a lesser extent, likely pathogenic variants (64.1%%; 50/78 received answers), were included in the ECS report for individuals and couples undergoing MAR with their own gametes. According to 87.9% (80/91 received answers) of the respondents, patients have to pay to undergo an ECS test. Most respondents (76.2%; 61/80 received answers) reported that counselling is provided before and after the ECS test. Preimplantation genetic testing, the use of donor gametes, and prenatal diagnostic testing were the three main reproductive options discussed with identified carrier couples. The main reason, according to the respondents, for not offering ECS in their centre, was the lack of professional recommendations supporting ECS (52.5%; 73/139 received answers) and the high cost for couples or reimbursement not being available (49.6%; 69/139). The challenges and moral dilemmas encountered by the respondents revolved mainly around the content of the offer, including the variants classification and the heterogeneity of the panels, the counselling, and the cost of the test.

LIMITATIONS, REASONS FOR CAUTION

Although the total number of respondents was acceptable, the completion rate of the survey was suboptimal. In addition, the heterogeneity of answers to open-ended questions and the ambiguity of some of the answers, along with incomplete responses, posed a challenge in interpreting survey results. It is also plausible that some questions were not easily understood by the respondents. For this reason, response and non-response bias are acknowledged as further limitations of the survey.

WIDER IMPLICATIONS OF THE FINDINGS

The results of this survey could aid in identifying potential challenges or areas for improvement in the current practice of ECS in the MAR field and contribute to the discussion on how to address them. The results underline the need to stimulate a more knowledge-based debate on the complexity and the pros and cons of a possible implementation of ECS in MAR.

STUDY FUNDING/COMPETING INTEREST(S)

All costs relating to the development process were covered from European Society of Human Reproduction and Embryology and European Society of Human Genetics funds. There was no external funding of the development process or manuscript production. A.C. is full-time employee of Juno Genetics. L.H. declared receiving a research grant during the past 36 months from the Netherlands Organisation for Health Research and Development. She has also participated in a Health Council report of the Netherlands on preconception carrier screening and collaborated with the VSOP Dutch Genetic Alliance (patient umbrella organization on rare and genetic disorders). L.H. and C.v.E. are affiliated with Amsterdam University Medical Centre, a hospital that offers ECS in a non-commercial setting. R.V. received honoraria for presentations from Merck Academy and is unpaid board member of the executive committee of the Spanish Fertility Society. The other authors had nothing to disclose.

TRIAL REGISTRATION NUMBER

N/A.

Expectations, needs and mid-term outcomes in people accessing to secondary findings from ES: 1st French mixed study (FIND Study)

Generation and subsequently accessibility of secondary findings (SF) in diagnostic practice is a subject of debate around the world and particularly in Europe. The French FIND study has been set up to assess patient/parent expectations regarding SF from exome sequencing (ES) and to collect their real-life experience until 1 year after the delivery of results. 340 patients who had ES for undiagnosed developmental disorders were included in this multicenter mixed study (quantitative N = 340; qualitative N = 26). Three groups of actionable SF were rendered: predisposition to late-onset actionable diseases; genetic counseling; pharmacogenomics. Participants expressed strong interest in obtaining SF and a high satisfaction level when a SF is reported. The medical actionability of the SF reinforced parents' sense of taking action for their child and was seen as an opportunity. While we observed no serious psychological concerns, we showed that these results could have psychological consequences, in particular for late-onset actionable diseases SF, within families already dealing with rare diseases. This study shows that participants remain in favor of accessing SF despite the potential psychological, care, and lifestyle impacts, which are difficult to anticipate. The establishment of a management protocol, including the support of a multidisciplinary team, would be necessary if national policy allows the reporting of these data.

An Integrated Framework for Analysis and Prediction of Impact of Single Nucleotide Polymorphism Associated with Human Diseases

Single nucleotide polymorphisms are most common type of genetic variation in human genome. Analyzing genetic variants can help us better understand the genetic basis of diseases and develop predictive models which are useful to identify individuals who are at increased risk for certain diseases. Several SNP analysis tools have already been developed. For running these tools, the user needs to collect data from various databases. Secondly, often researchers have to use multiple variant analysis tools for cross validating their results and increase confidence in their findings. Extracting data from multiple databases and running multiple tools at a time, increases complexity and time required for analysis. There are some web-based tools that integrate multiple genetic variant databases and provide variant annotations for a few tools. These approaches have some limitations such as retrieving annotation information, filtering common pathogenic variants. The proposed web-based tool, namely IPSNP: An Integrated Platform for Predicting Impact of SNPs is written in Django which is a python-based framework. It uses RESTful API of MyVariant.info to extract annotation information of variants associated with a given gene, rsID, HGVS format variants specified in a VCF file for 29 tools. The results are in the form of a CSV file of predictions (1) derived from the consensus decision, (2) a file having annotations for the variants associated with the given gene, (3) a file showing variants declared as pathogenic commonly by the selected tools, and (4) a CSV file containing chromosome coordinates based on GRCh37 and GRCh38 genome assemblies, rsIDs and proteomic data, so that users may use tools of their choice and avoiding manual parameter collection for each tool. IPSNP is a valuable resource for researchers and clinicians and it can help to save time and effort in discovering the novel disease-associated variants and the development of personalized treatments.

Disclosure of genetic risk to family members: A qualitative study on healthcare professionals' perceived roles and responsibilities

This paper presents the perspectives of healthcare professionals regarding their roles and responsibilities in supporting patients with the disclosure of genetic risk to their families. The study involved eight focus groups and two individual interviews with 34 healthcare professionals working in medical genetics services across Portugal. The data were analyzed thematically, resulting in three primary themes: i) informing patients about the risk to relatives; ii) ensuring patient confidentiality; and iii) encouraging family communication. Participants believed it is their responsibility to inform patients about the genetic risk to their relatives, with patients bearing a moral responsibility to convey this information. They explained that the principles of medical confidentiality of the patient take precedence over any direct responsibility to patients' relatives. Treating personal and familial genetic information separately was perceived as challenging to implement and potentially problematic. While most participants reported encouraging patients to inform their relatives, the extent to which they facilitate this communication varies and is also constrained by lack of resources and concerns about complying with legal requirements. Some participants called for clearer national guidelines. These results contribute for ongoing discussions regarding the scope of practice and the roles and responsibilities of healthcare professionals in appropriately cascading pertinent information to at-risk relatives.

Glucose phosphate isomerase deficiency demasked by whole-genome sequencing: a case report

BACKGROUND

Glucose-6-phosphate isomerase deficiency is a rare genetic disorder causing hereditary nonspherocytic hemolytic anemia. It is the second most common glycolytic enzymopathy in red blood cells. About 90 cases are reported worldwide, with symptoms including chronic hemolytic anemia, jaundice, splenomegaly, gallstones, cholecystitis, and in severe cases, neurological impairments, hydrops fetalis, and neonatal death.

CASE PRESENTATION

This paper details the case of the first Danish patient diagnosed with glucose-6-phosphate isomerase deficiency. The patient, a 27-year-old white female, suffered from lifelong anemia of unknown origin for decades. Diagnosis was established through whole-genome sequencing, which identified two GPI missense variants: the previously documented variant p.(Thr224Met) and a newly discovered variant p.(Tyr341Cys). The pathogenicity of these variants was verified enzymatically.

CONCLUSIONS

Whole-genome sequencing stands as a potent tool for identifying hereditary anemias, ensuring optimal management strategies.

Hope, but never expect? Comparing parents' pre- and post-disclosure attitudes toward return of results from diagnostic exome sequencing for their child

BACKGROUND

Counseling for whole-exome sequencing (WES) could benefit from aligning parents' pre- and post-disclosure attitudes. A few studies have qualitatively compared parents' pre- and post-disclosure attitudes toward receiving WES results for their child in a diagnostic setting. This study explored these attitudes in the context of children with a developmental delay.

METHODS

Semi-structured interviews were conducted with parents (n = 27) of 16 children undergoing diagnostic WES in trio-analysis, both before and after receiving results.

RESULTS

Three key insights emerged. First, the distinction between hoping and expecting was relevant for shaping parents' experiences with receiving results related to the primary indication. Second, parents of young children whose development of autonomous capacities was uncertain sometimes found themselves in a situation resembling a Catch-22 when confronted with decisions about unsolicited findings (UFs): an important reason for consenting to WES was to gain a better picture of how the child might develop, but in order to make responsible choices about UFs, some ideas of their child's development is needed. Third, default opt-ins and opt-outs helped parents fathom new kinds of considerations for accepting or declining UFs in different categories, thereby aiding decision-making.

CONCLUSION

Results from this study are relevant for counseling and policy development.

Secondary (additional) findings from the 100,000 Genomes Project: Disease manifestation, health care outcomes, and costs of disclosure

PURPOSE

The UK 100,000 Genomes Project offered participants screening for additional findings (AFs) in genes associated with familial hypercholesterolemia (FH) or hereditary cancer syndromes including breast/ovarian cancer (HBOC), Lynch, familial adenomatous polyposis, MYH-associated polyposis, multiple endocrine neoplasia (MEN), and von Hippel-Lindau. Here, we report disclosure processes, manifestation of AF-related disease, outcomes, and costs.

METHODS

An observational study in an area representing one-fifth of England.

RESULTS

Data were collected from 89 adult AF recipients. At disclosure, among 57 recipients of a cancer-predisposition-associated AF and 32 recipients of an FH-associated AF, 35% and 88%, respectively, had personal and/or family history evidence of AF-related disease. During post-disclosure investigations, 4 cancer-AF recipients had evidence of disease, including 1 medullary thyroid cancer. Six women with an HBOC AF, 3 women with a Lynch syndrome AF, and 2 individuals with a MEN AF elected for risk-reducing surgery. New hyperlipidemia diagnoses were made in 6 FH-AF recipients and treatment (re-)initiated for 7 with prior hyperlipidemia. Generating and disclosing AFs in this region cost £1.4m; £8680 per clinically significant AF.

CONCLUSION

Generation and disclosure of AFs identifies individuals with and without personal or familial evidence of disease and prompts appropriate clinical interventions. Results can inform policy toward secondary findings.

Parents' attitudes towards research involving genome sequencing of their healthy children: a qualitative study

With widespread genomic sequencing research efforts, there is increasing impetus to return results to participants. Parents of healthy children are increasingly asked to participate in genomic research, yet there are limited studies of parental expectations for the return of results amongst healthy children. We explored parental attitudes towards their healthy children's participation in genomic research and expectations for return of results. Data collection involved semi-structured telephone interviews with parents of healthy children participating in a primary care research network. Transcripts were analyzed thematically using constant comparison. A total of 26 parents were interviewed: 22 were female, 19 self-reported as White/European, and 20 were aged 30-39. Three themes emerged: (1) Reciprocity; Parents preferred to receive medically actionable, childhood-onset results and expected recontact overtime in exchange for their research participation. (2) Downstream impacts of testing; Parents expected future clinical benefits but were concerned about the risk of genetic discrimination. (3) Power and empowerment; Some parents felt empowered to take preventative action for their child and relatives, while others did not want to limit their child's autonomy. Considering these tensions may help to inform participant-centered approaches to optimize parental decision-making and participation, as well as maximize the utility of results.

Artificial intelligence and database for NGS-based diagnosis in rare disease

Rare diseases (RDs) are rare complex genetic diseases affecting a conservative estimate of 300 million people worldwide. Recent Next-Generation Sequencing (NGS) studies are unraveling the underlying genetic heterogeneity of this group of diseases. NGS-based methods used in RDs studies have improved the diagnosis and management of RDs. Concomitantly, a suite of bioinformatics tools has been developed to sort through big data generated by NGS to understand RDs better. However, there are concerns regarding the lack of consistency among different methods, primarily linked to factors such as the lack of uniformity in input and output formats, the absence of a standardized measure for predictive accuracy, and the regularity of updates to the annotation database. Today, artificial intelligence (AI), particularly deep learning, is widely used in a variety of biological contexts, changing the healthcare system. AI has demonstrated promising capabilities in boosting variant calling precision, refining variant prediction, and enhancing the user-friendliness of electronic health record (EHR) systems in NGS-based diagnostics. This paper reviews the state of the art of AI in NGS-based genetics, and its future directions and challenges. It also compare several rare disease databases.

Human Genetics of Congenital Heart Defects

Congenital heart diseases (or congenital heart defects/disorders; CHDs) are structural abnormalities of the heart and/or great vessels that are present at birth. CHDs include an extensive range of defects that may be minor and require no intervention or may be life-limiting and require complex surgery shortly after birth. This chapter reviews the current knowledge on the genetic causes of CHD.

Chapitre 5. From individuals to social: The needs for a global ethics overview in pharmacogenomics

As a part of personalized medicine, pharmacogenomics (PGx) allows practitioners to provide the right drug for a given patient, in accordance with the result of a genetic test. This practice raises many ethical issues that are discussed in the literature, sometimes within the larger context of personalized medicine. This article is based on a literature review that is original insofar as it is interdisciplinary and based on an approach that articulates individual and social rights. Here, we propose to reconsider some classic ethical issues, such as informed consent, incidental findings and data protection which are raised by genetic testing and also by PGx in the same or in a different way. We also analyse broader collective issues around racialization and health equality. Our purpose is to contribute in drawing links and parallels between individual rights and collective rights using a social approach. This analysis discusses these ethical issues in research and in clinical setting, understanding the treatment of the individual in his dual quality of patient and research participant.

Dealing with ambivalence in the practice of advanced genetic healthcare: towards an ethical choreography

The implementation of next-generation sequencing (NGS) in diagnostic practice has stimulated ongoing debates on how to construct and perform "good" genomic care. Our multi-sited qualitative fieldwork at two large European centres for human genetics (CHGs) revealed tangible ambivalence in beliefs, norms, and actions in the enactment of NGS practices across sites stemming from differing expectations, interests, demands, and tensions. First, ambivalence was present around the boundaries of clinical diagnostic genetic care. The overlap between research and clinical work and diagnostics and screening led to ambivalence around "best" practices and norms concerning whom to offer NGS testing and how far to take testing. Secondly, the clinical value of NGS results, especially VUS and unsolicited findings, was ambivalently valued, resulting in an inconsistent approach towards these types of findings. Thirdly, ambivalence was recognized in applying guidelines in the reality of clinical practice. The ambivalence we encountered was often not made explicit or acknowledged, causing a failure to benefit from its possibility to encourage reflexivity and change. We propose to facilitate a more explicit ethical choreography [27], where ethics and science are developed iteratively whilst welcoming different perspectives and disciplines. Pulling experiences and practices of ambivalence into the light can help to understand the points of tension in the values and internal logic in care practices within the CHGs and facilitate a more informed, transparent, and consciously chosen direction for genetic care.

Uncertain futures and unsolicited findings in pediatric genomic sequencing: guidelines for return of results in cases of developmental delay

BACKGROUND

Massively parallel sequencing techniques, such as whole exome sequencing (WES) and whole genome sequencing (WGS), may reveal unsolicited findings (UFs) unrelated to the diagnostic aim. Such techniques are frequently used for diagnostic purposes in pediatric cases of developmental delay (DD). Yet policy guidelines for informed consent and return of UFs are not well equipped to address specific moral challenges that may arise in these children's situations.

DISCUSSION

In previous empirical studies conducted by our research group, we found that it is sometimes uncertain how children with a DD will develop and whether they could come to possess capacities for autonomous decision-making in the future. Parents sometimes felt this brought them into a Catch-22 like situation when confronted with choices about UFs before undergoing WES in trio-analysis (both the parents' and child's DNA are sequenced). An important reason for choosing to consent to WES was to gain more insight into how their child might develop. However, to make responsible choices about receiving or declining knowledge of UFs, some idea of their child's future development of autonomous capacities is needed. This undesirable Catch-22 situation was created by the specific policy configuration in which parents were required to make choices about UFs before being sequencing (trio-analysis). We argue that this finding is relevant for reconfiguring current policies for return of UFs for WES/WGS and propose guidelines that encompass two features. First, the informed consent process ought to be staged. Second, differing guidelines are required for withholding/disclosing a UF in cases of DD appropriate to the level of confidence there is about the child's future developmental of autonomous capacities.

CONCLUSION

When combined with a dynamic consent procedure, these two features of our guidelines could help overcome significant moral challenges that present themselves in the situations of children undergoing genomic sequencing for clarifying a DD.

Frequency of actionable secondary findings in 7472 Korean genomes derived from the National Project of Bio Big Data pilot study

Exome and genome sequencing (ES/GS) in genetic medicine and research leads to discovering genomic secondary findings (SFs) unrelated to the purpose of the primary test. There is a lack of agreement to return the SF results for individuals undergoing the test. The aim of this study is to investigate the frequency of actionable secondary findings using GS data obtained from the rare disease study and the Korean Genome and Epidemiology Study (KoGES) in the National Project of Bio Big Data pilot study. Pathogenic (P) or likely pathogenic (LP) variants of 78 SF genes recommended by the American College of Medical Genetics and Genomics (ACMG) were screened in the rare disease study and KoGES. The pathogenicity of SF gene variants was determined according to the ACMG interpretation. The overall SF rate was 3.75% for 280 individuals with 298 P/LP variants of 41 ACMG SF genes which were identified among 7472 study participants. The frequencies of genes associated with cardiovascular, cancer, and miscellaneous phenotypes were 2.17%, 1.22%, and 0.58%, respectively. The most frequent SF gene was TTN followed by BRCA2. The frequency of actionable SFs among participants with rare disease and general population participants in the Korean population presented here will assist in reporting results of medically actionable SFs in genomic medicine.

What's in a name? Justifying terminology for genomic findings beyond the initial test indication: A scoping review

Genome sequencing can generate findings beyond the initial test indication that may be relevant to a patient or research participant's health. In the decade since the American College of Medical Genetics and Genomics published its recommendations for reporting these findings, consensus regarding terminology has remained elusive and a variety of terms are in use globally. We conducted a scoping review to explore terminology choice and the justifications underlying those choices. Documents were included if they contained a justification for their choice of term(s) related to findings beyond the initial genomic test indication. From 3571 unique documents, 52 were included, just over half of which pertained to the clinical context (n = 29, 56%). We identified four inter-related concepts used to defend or oppose terms: expectedness of the finding, effective communication, relatedness to the original test indication, and how genomic information was generated. A variety of justifications were used to oppose the term "incidental," whereas "secondary" had broader support as a term to describe findings deliberately sought. Terminology choice would benefit from further work to include the views of patients. We contend that clear definitions will improve ethical debate and support communication about genomic findings beyond the initial test indication.

Exome and genome sequencing for rare genetic disease diagnosis: A scoping review and critical appraisal of clinical guidance documents produced by genetics professional organizations

PURPOSE

Exome and genome sequencing have rapidly transitioned from research methods to widely used clinical tests for diagnosing rare genetic diseases. We sought to synthesize the topics covered and appraise the development processes of clinical guidance documents generated by genetics professional organizations.

METHODS

We conducted a scoping review of guidance documents published since 2010, systematically identified in peer-reviewed and gray literature, using established methods and reporting guidelines. We coded verbatim recommendations by topic using content analysis and critically appraised documents using the Appraisal of Guidelines Research and Evaluation (AGREE) II tool.

RESULTS

We identified 30 guidance documents produced by 8 organizations (2012-2022), yielding 611 recommendations covering 21 topics. The most common topic related to findings beyond the primary testing indication. Mean AGREE II scores were low across all 6 quality domains; scores for items related to rigor of development were among the lowest. More recently published documents generally received higher scores.

CONCLUSION

Guidance documents included a broad range of recommendations but were of low quality, particularly in their rigor of development. Developers should consider using tools such as AGREE II and basing recommendations on living knowledge syntheses to improve guidance development in this evolving space.

A qualitative process evaluation using the behaviour change wheel approach: Did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated?

PURPOSE

The aim of this study was to conduct a process evaluation of a whole-genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours within the COVID-19 pandemic.

METHODS

We used a three-staged design. Firstly, we described and theorized the purported content of the SRF using the behaviour change wheel (BCW). Secondly, we used inductive thematic analysis of one-to-one interviews (n = 39) to explore contextual accounts of using the SRF. Thirdly, further deductive analysis gauged support for the intervention working as earlier anticipated.

RESULTS

It was possible to theorize the SRF using the BCW approach and visualize it within a simple logic model. Inductive thematic analyses identified the SRF's acceptability, ease of use and perceived effectiveness. However, major challenges to embedding it in routine practice during the unfolding COVID-19 crisis were reported. Notwithstanding this insight, deductive analysis showed support for the putative intervention functions 'Education', 'Persuasion' and 'Enablement'; behaviour change techniques '1.2 Problem solving', '2.6 Biofeedback', '2.7 Feedback on outcomes of behaviour' and '7.1 Prompts and cues'; and theoretical domains framework domains 'Knowledge' and 'Behavioural regulation'.

CONCLUSIONS

Our process evaluation of the SRF, using the BCW approach to describe and theorize its content, provided granular support for the SRF working to change IPC behaviours as anticipated. However, our complementary inductive thematic analysis highlighted the importance of the local context in constraining its routine use. For SRFs to reach their full potential in reducing nosocomial infections, further implementation research is needed.

Precision medicine in rare diseases: What is next?

Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.

The role of a multidisciplinary team in managing variants of uncertain clinical significance in prenatal genetic diagnosis

BACKGROUND

Although in general prenatal exome sequencing only reports (likely) pathogenic variants, in some cases a variant of uncertain significance (VUS) is disclosed. The aims of this retrospective study were to evaluate the types of VUS that have been reported to prospective parents, possible reclassification and to design a standard flow chart to determine which types of VUS could be considered for reporting in prenatal settings. Furthermore, we investigated what the crucial elements are to facilitate rapid management of uncertain results in a prenatal setting.

MATERIAL AND METHODS

We reviewed exome results from 451 pregnancies performed in 2019-2021. We analyzed which factors that were taken into account by the multidisciplinary team (MDT) contributed towards decision making on reporting VUS after prenatal exome sequencing.

RESULTS

In 9/451 (2%) pregnancies tested with exome sequencing using a broad panel analysis a VUS was reported. After birth 3/9 VUS could be reclassified to likely pathogenic variants based on new clinical follow up data. We considered reporting VUS in genes: 1) matching the fetal phenotype, 2) associated with a severe disorder when a functional test is available or 3) possibly associated with a disorder where early post-partum diagnosis and treatment are crucial for a better prognosis. Two flowcharts were designed to guide first the laboratory specialist and then the MDT in decisions on reporting VUS. The crucial elements that enabled timely decisions on VUS disclosure were regular meetings, appropriate expertise, professional connections with other experts and psychological safety within the MDT.

CONCLUSION

In this study three out of nine VUS could be re-classified as likely pathogenic after clinical follow-up. In order to protect pregnant couples from the burden of uncertain results, the genetic professionals have to take the responsibility to limit the reporting of VUS. This can be done not only by automated filtering of data, by following professional guidelines and by building standardized decision flows, but also by discussing individual cases considering personal situations and the involved disease and by sharing professional experience and responsibility in a multidisciplinary prenatal team setting.

Protocol for a Prospective, Observational Cost-effectiveness Analysis of Returning Secondary Findings of Genome Sequencing for Unexplained Suspected Genetic Conditions

PURPOSE

Although costly, genome-wide sequencing (GWS) detects an extensive range of variants, enhancing our ability to diagnose and assess risk for an increasing number of diseases. In addition to detecting variants related to the indication for testing, GWS can detect secondary variants in BRCA1, BRCA2, and other genes for which early intervention may improve health. As the list of secondary findings grows, there is increased demand for surveillance and management by multiple specialists, adding pressure to constrained health care budgets. Secondary finding testing is actively debated because some consider it opportunistic screening for future health risks that may not manifest. Given the economic implications of secondary finding testing and follow-up and its unproven clinical utility, the objective is to assess the incremental cost-effectiveness of secondary finding ascertainment per case detected and per unit of improved clinical utility in families of children with unexplained suspected genetic conditions undergoing clinical GWS.

METHODS

Those undergoing trio genome or exome sequencing are eligible for the study. Positive secondary finding index cases will be matched to negative controls (1:2) based on age group, primary result(s) type, and clinical indication. During the 2-year study, 71 cases and 142 matched controls are expected. Health service use will be collected in patients and 1 adult family member every 6 months. The per-child and per-dyad total cost will be determined by multiplying use of each resource by a corresponding unit price and summing all cost items. Costs will be estimated from the public and societal payer perspectives. The mean cost per child and per dyad for secondary finding-positive and secondary finding-negative groups will be compared statistically. If important demographic differences are observed between groups, ordinary least-squares regression, log transformation, or other nonparametric technique will be used to compare adjusted mean costs. The ratio of the difference in mean cost to the secondary finding yield will be used to estimate incremental cost-effectiveness. In secondary analyses, effectiveness will be estimated using the number of clinical management changes due to secondary findings or the Clinician-Reported Genetic Testing Utility Index (C-GUIDE) score, a validated measure of clinical utility. Sensitivity analysis will be undertaken to assess the robustness of the findings to variation in key parameters.

IMPLICATIONS

This study generates key evidence to inform clinical practice and funding allocation related to secondary finding testing. The inclusion of family members and a new measure of clinical utility represent important advancements in economic evaluation in genomics.

Two-step offer and return of multiple types of additional genomic findings to families after ultrarapid trio genomic testing in the acute care setting: a study protocol

INTRODUCTION

As routine genomic testing expands, so too does the opportunity to look for additional health information unrelated to the original reason for testing, termed additional findings (AF). Analysis for many different types of AF may be available, particularly to families undergoing trio genomic testing. The optimal model for service delivery remains to be determined, especially when the original test occurs in the acute care setting.

METHODS AND ANALYSIS

Families enrolled in a national study providing ultrarapid genomic testing to critically ill children will be offered analysis for three types of AF on their stored genomic data: paediatric-onset conditions in the child, adult-onset conditions in each parent and reproductive carrier screening for the parents as a couple. The offer will be made 3-6 months after diagnostic testing. Parents will have access to a modified version of the Genetics Adviser web-based decision support tool before attending a genetic counselling appointment to discuss consent for AF. Parental experiences will be evaluated using qualitative and quantitative methods on data collected through surveys, appointment recordings and interviews at multiple time points. Evaluation will focus on parental preferences, uptake, decision support use and understanding of AF. Genetic health professionals' perspectives on acceptability and feasibility of AF will also be captured through surveys and interviews.

ETHICS AND DISSEMINATION

This project received ethics approval from the Melbourne Health Human Research Ethics Committee as part of the Australian Genomics Health Alliance protocol: HREC/16/MH/251. Findings will be disseminated through peer-review journal articles and at conferences nationally and internationally.

Consensus Statements on Precision Oncology in the China Greater Bay Area

BACKGROUND

Next-generation sequencing comprehensive genomic panels (NGS CGPs) have enabled the delivery of tailor-made therapeutic approaches to improve survival outcomes in patients with cancer. Within the China Greater Bay Area (GBA), territorial differences in clinical practices and health care systems and strengthening collaboration warrant a regional consensus to consolidate the development and integration of precision oncology (PO). Therefore, the Precision Oncology Working Group (POWG) formulated standardized principles for the clinical application of molecular profiling, interpretation of genomic alterations, and alignment of actionable mutations with sequence-directed therapy to deliver clinical services of excellence and evidence-based care to patients with cancer in the China GBA.

METHODS

Thirty experts used a modified Delphi method. The evidence extracted to support the statements was graded according to the GRADE system and reported according to the Revised Standards for Quality Improvement Reporting Excellence guidelines, version 2.0.

RESULTS

The POWG reached consensus in six key statements: harmonization of reporting and quality assurance of NGS; molecular tumor board and clinical decision support systems for PO; education and training; research and real-world data collection, patient engagement, regulations, and financial reimbursement of PO treatment strategies; and clinical recommendations and implementation of PO in clinical practice.

CONCLUSION

POWG consensus statements standardize the clinical application of NGS CGPs, streamline the interpretation of clinically significant genomic alterations, and align actionable mutations with sequence-directed therapies. The POWG consensus statements may harmonize the utility and delivery of PO in China's GBA.

A practical checklist for return of results from genomic research in the European context

An increasing number of European research projects return, or plan to return, individual genomic research results (IRR) to participants. While data access is a data subject's right under the General Data Protection Regulation (GDPR), and many legal and ethical guidelines allow or require participants to receive personal data generated in research, the practice of returning results is not straightforward and raises several practical and ethical issues. Existing guidelines focusing on return of IRR are mostly project-specific, only discuss which results to return, or were developed outside Europe. To address this gap, we analysed existing normative documents identified online using inductive content analysis. We used this analysis to develop a checklist of steps to assist European researchers considering whether to return IRR to participants. We then sought feedback on the checklist from an interdisciplinary panel of European experts (clinicians, clinical researchers, population-based researchers, biobank managers, ethicists, lawyers and policy makers) to refine the checklist. The checklist outlines seven major components researchers should consider when determining whether, and how, to return results to adult research participants: 1) Decide which results to return; 2) Develop a plan for return of results; 3) Obtain participant informed consent; 4) Collect and analyse data; 5) Confirm results; 6) Disclose research results; 7) Follow-up and monitor. Our checklist provides a clear outline of the steps European researchers can follow to develop ethical and sustainable result return pathways within their own research projects. Further legal analysis is required to ensure this checklist complies with relevant domestic laws.

An Optimal Stacked ResNet-BiLSTM-Based Accurate Detection and Classification of Genetic Disorders

Gene is located inside the nuclease and the genetic data is contained in deoxyribonucleic acid (DNA). A person's gene count ranges from 20,000 to 30,000. Even a minor alteration to the DNA sequence can be harmful if it affects the cell's fundamental functions. As a result, the gene begins to act abnormally. The sorts of genetic abnormalities brought on by mutation include chromosomal disorders, complex disorders, and single-gene disorders. Therefore, a detailed diagnosis method is required. Thus, we proposed an Elephant Herd Optimization-Whale Optimization Algorithm (EHO-WOA) optimized Stacked ResNet-Bidirectional Long Term Short Memory (ResNet-BiLSTM) model for detecting genetic disorders. Here, a hybrid EHO-WOA algorithm is presented to assess the Stacked ResNet-BiLSTM architecture's fitness. The ResNet-BiLSTM design uses the genotype and gene expression phenotype as input data. Furthermore, the proposed method identifies rare genetic disorders such as Angelman Syndrome, Rett Syndrome, and Prader-Willi Syndrome. It demonstrates the effectiveness of the developed model with greater accuracy, recall, specificity, precision, and f1-score. Thus, a wide range of DNA deficiencies including Prader-Willi syndrome, Marfan syndrome, Early Onset Morbid Obesity, Rett syndrome, and Angelman syndrome are predicted accurately.

Challenges and Pragmatic Solutions in Pre-Test and Post-Test Genetic Counseling for Prenatal Exome Sequencing

The yield of genetic prenatal diagnosis has been notably improved by introducing whole genome chromosomal microarray (CMA) and prenatal exome sequencing (pES). However, together with increased numbers of diagnoses made, the need to manage challenging findings such as variants of unknown significance (VUS) and incidental findings (IF) also increased. We have summarized the current guidelines and recommendations and we have shown current solutions used in our tertiary center in the Netherlands. We discuss four of the most common clinical situations: fetus with normal pES results, fetus with a pathogenic finding explaining the fetal phenotype, fetus with a variant of uncertain clinical significance fitting the phenotype and fetus with a variant leading to an incidental diagnosis. Additionally, we reflect on solutions in order to facilitate genetic counseling in an NGS-era.

High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders

Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.

Recontact: a survey of current practices and BRCA1/2 testing in Japan

Genetic testing advances have enabled the provision of previously unavailable information on the pathogenicity of genetic variants, frequently necessitating the recontact of former patients by clinicians. In Japan, national health insurance coverage was extended to BRCA1/2 testing for the diagnosis of hereditary breast and ovarian cancer for patients who meet certain criteria in 2020, and conditions necessitating recontact were expected to increase. Studies and discussions regarding recontact have been conducted in the U.S. and Europe; however, in Japan, the national discussion around recontact remains undeveloped. We conducted a cross-sectional study by interviewing 73 facilities accredited by the Japanese Organization of Hereditary Breast and Ovarian Cancer regarding the practice of recontacting patients at these facilities. Sixty-six facilities responded that they recontact patients, but only 17 facilities had a protocol for this. The most common reason for recontact was that it could benefit the patient. Facilities that did not recontact stated that they lacked the necessary personnel or services. Most facilities indicated that a recontact system should be implemented in their practice. The increased burden on too few medical personnel, unestablished systems, patient confusion, and the right not to know were cited as barriers to implementing recontact. Although developing recommendations on recontact would be useful for providing equitable healthcare in Japan, there is an urgent need to deepen the discussion on recontacting, as negative opinions about recontacting patients were observed.

Decoding the mechanism of hypertension through multiomics profiling

Hypertension, characterised by a constant high blood pressure, is the primary risk factor for multiple cardiovascular events and a major cause of death in adults. Excitingly, innovations in high-throughput technologies have enabled the global exploration of the whole genome (genomics), revealing dysregulated genes that are linked to hypertension. Moreover, post-genomic biomarkers, from the emerging fields of transcriptomics, proteomics, glycomics and lipidomics, have provided new insights into the molecular underpinnings of hypertension. In this paper, we review the pathophysiology of hypertension, and highlight the multi-omics approaches for hypertension prediction and diagnosis.

Great expectations: patients' preferences for clinically significant results from genomic sequencing

We aimed to describe patient preferences for a broad range of secondary findings (SF) from genomic sequencing (GS) and factors driving preferences. We assessed preference data within a trial of the Genomics ADvISER, (SF decision aid) among adult cancer patients. Participants could choose from five categories of SF: (1) medically actionable; (2) polygenic risks; (3) rare diseases; (4) early-onset neurological diseases; and (5) carrier status. We analyzed preferences using descriptive statistics and drivers of preferences using multivariable logistic regression models. The 133 participants were predominantly European (74%) or East Asian or mixed ancestry (13%), female (90%), and aged > 50 years old (60%). The majority chose to receive SF. 97% (129/133) chose actionable findings with 36% (48/133) choosing all 5 categories. Despite the lack of medical actionability, participants were interested in receiving SF of polygenic risks (74%), carrier status (75%), rare diseases (59%), and early-onset neurologic diseases (53%). Older participants were more likely to be interested in receiving results for early-onset neurological diseases, while those exhibiting lower decisional conflict were more likely to select all categories. Our results highlight a disconnect between cancer patient preferences and professional guidelines on SF, such as ACMG's recommendations to only return medically actionable secondary findings. In addition to clinical evidence, future guidelines should incorporate patient preferences.

Phenotypic and genotypic survey of antibiotic resistance in Salmonella enterica isolates from dairy farms in Uruguay

Salmonella enterica is an important zoonotic pathogen that is frequently identified in dairy farming systems. An increase in antibiotic resistance has led to inadequate results of treatments, with impacts on animal and human health. Here, the phenotypic and genotypic susceptibility patterns of Salmonella isolates from dairy cattle and dairy farm environments were evaluated and compared. A collection of 75 S. enterica isolates were evaluated, and their phenotypic susceptibility was determined. For genotypic characterization, the whole genomes of the isolates were sequenced, and geno-serotypes, sequence types (STs) and core-genome-sequence types were determined using the EnteroBase pipeline. To characterize antibiotic resistance genes and gene mutations, tools from the Center for Genomic Epidemiology were used. Salmonella Dublin (SDu), S. Typhimurium (STy), S. Anatum (SAn), S. Newport (SNe), S. Agona (Sag), S. Montevideo (SMo) and IIIb 61:i:z53 were included in the collection. A single sequence type was detected per serovar. Phenotypic non-susceptibility to streptomycin and tetracycline was very frequent in the collection, and high non-susceptibility to ciprofloxacin was also observed. Multidrug resistance (MDR) was observed in 42 isolates (56.0%), with SAn and STy presenting higher MDR than the other serovars, showing non-susceptibility to up to 6 groups of antibiotics. Genomic analysis revealed the presence of 21 genes associated with antimicrobial resistance (AMR) in Salmonella isolates. More than 60% of the isolates carried some gene associated with resistance to aminoglycosides and tetracyclines. Only one gene associated with beta-lactam resistance was found, in seven isolates. Two different mutations were identified, parC_T57S and acrB_R717Q, which confer resistance to quinolones and azithromycin, respectively. The accuracy of predicting antimicrobial resistance phenotypes based on AMR genotypes was 83.7%. The genomic approach does not replace the phenotypic assay but offers valuable information for the survey of circulating antimicrobial resistance. This work represents one of the first studies evaluating phenotypic and genotypic AMR in Salmonella from dairy cattle in South America.

Do genomic passports leave us more vulnerable or less vulnerable? Perspectives from an online citizen engagement

Since genomics is becoming commonplace in healthcare for the diagnosis, treatment, and prevention, the prospect of generating a genomic passport for all citizens is gaining traction. While this would have many advantages, it raises ethical issues requiring societal debate alongside academic reflection. Hence, Sciensano-the Belgian scientific Institute of Public Health-organised an online citizen engagement on genomic information usage, including a question on a genomic passport for all. The inductive thematic analysis of participants' contributions highlighted vulnerability as a fundamental concern, while this has not received sufficient attention so far in genomics. Participants expressed their vulnerability in two ways. First, the genomic passport would inform them about their ontological vulnerability. By revealing their constitutional weaknesses (predisposition to diseases), it reminds them that everyone is unavoidably and perennially at risk of being harmed. Second, the misuse of the genomic passport can add situational vulnerabilities (e.g., discrimination causing psychological and economic harm). Moreover, the fundamental uncertainty in genomics-how will such sensitive information be used, and how will the science evolve?-exacerbates these vulnerabilities. This article ends with recommendations to alleviate these vulnerabilities in genomics now and in the future in which the genomic passport may become a reality.

An spanish study of secondary findings in families affected with mendelian disorders: choices, prevalence and family history

Clinical exome sequencing has the potential to identify pathogenic variants unrelated to the purpose of the study (secondary findings, SFs). Data describing actual choices of SFs in participants in a clinical setting and factors influencing their decision are virtually non-existant in Europe. In this work, we report the acceptance rate of SFs, calculate their prevalence and study factors associated with the decision in a cohort of patients affected with a rare genetic disorder in a Spanish Hospital. Finally, we re-examine the presence of previously non reported family history in positive cases. We retrospectively reviewed informed consent choices and SF results from 824 unrelated probands affected with rare genetic disorders who underwent whole-genome or exome sequencing. Ninety percent of families (740/824) affected with rare disorders wished to be informed of SFs. Declining SFs was associated with a prenatal setting (30% vs. 8.7%, p = 0.025), consanguinity (19% vs. 8.7%, p = 0.013), male gender (10.6% vs. 1.5%, p = 0.00865) and the proband being a minor (10.6% vs. 1.5%, p = 0.014). Overall, 27 pathogenic or likely pathogenic variants were identified in 27 individuals, with an SF prevalence of 3.6%. Disclosure of SFs increased the percentage of positive family histories and resulted in early diagnosis or changes in the management of 10 individuals from five families. We show that the acceptance of SFs in Spain is high and the disclosure of SFs leads to a clinically meaningful change in the medical management of individuals.

Reporting clinically relevant genetic variants unrelated to genomic test requests: a survey of Australian clinical laboratory policies and practices

Approaches to reporting clinically important genetic findings unrelated to the initial test request vary internationally. We sought to investigate practices regarding the management and return of these findings in Australia. Australian clinically accredited genetic testing laboratories were surveyed in 2017 and 2020 regarding their opinions on issues relating to the return of clinically important genetic findings unrelated to the initial test request. Responses were collated and analysed for 15 laboratories in 2017, and 17 laboratories in 2020. Content analysis was also performed on seven laboratory policies in 2020. Analysis showed that overall there was a lack of consensus about the terminology used to describe such findings and reporting practices across different testing contexts. A clear exception was that no laboratories were actively searching for a list of medically actionable genes (eg, American College of Medical Genetics and Genomics secondary findings gene list). Laboratory policies showed little consistency in the documentation of issues related to the handling of these findings. These findings indicate a need for Australian-specific policy guidance that covers all aspects of clinically important genetic findings unrelated to the initial test request. We present recommendations for consideration when developing laboratory policies.

Heath policy guiding the identification, analysis and management of secondary findings for individuals undergoing genomic sequencing: a systematic review protocol

INTRODUCTION

Genomic sequencing is increasingly enabling precision care across medical specialties; however, the discovery of genomic 'secondary findings' (SFs) unrelated to the patient's primary indication remains a profuse, unintended consequence. Existing practices within the continuum of SF identification, analysis and management are numerous, inconsistent and sometimes contradictory across health conditions and regions. Final decisions are often at the discretion of the genomic sequencing laboratory, bioinformatician or treating physician. This difference in healthcare delivery causes inconsistent information, disclosure and downstream impacts required to manage SFs and patient outcomes. Improving our understanding of the SF health policy landscape can determine components of the SF policy continuum spanning generation through to management that are in conflict, limitations of current guidance and existing needs across clinical settings.

METHODS AND ANALYSIS

We will carry out a systematic review to catalogue and appraise current guidance directing the identification, analysis and management of SFs for participants receiving genomic sequencing globally. We will conduct a comprehensive search of Medline (Medline R, Medline Epub Ahead of Print and Medline-In-Process & In-Data-Review Citations), Embase and Cochrane databases (n=5, inception to Feb 2022) and a grey literature search of international genomics websites (n=64; inception to May 2022). Key inclusion criteria include: guidance produced by health organisations, bioethics committees and professional associations, outlining recommendations for: (1) SF identification, (2) SF analysis or (3) SF management. Non-English language articles and conference abstracts will be excluded. Guidance will be critically appraised with the Appraisal of Guidelines for Research & Evaluation Instrument (AGREE) II tool. We will interpret our findings by process and across populations using a qualitative descriptive approach.

ETHICS AND DISSEMINATION

Our systematic review evaluates published data and does not require ethics review. Our findings will be disseminated through peer-reviewed publications, conference presentations and workshops with precision medicine stakeholders.

PROSPERO REGISTRATION NUMBER

CRD42022316079.

Clinical exome-based panel testing for medically actionable secondary findings in a cohort of 383 Italian participants

Background: Next-generation sequencing-based genetic testing represents a great opportunity to identify hereditary predispositions to specific pathological conditions and to promptly implement health surveillance or therapeutic protocols in case of disease. The term secondary finding refers to the active search for causative variants in genes associated with medically actionable conditions.

Methods: We evaluated 59 medically actionable ACMG genes using a targeted in silico analysis of clinical exome sequencing performed in 383 consecutive individuals referred to our Medical Genetics Unit. A three-tier classification system of SFs for assessing their clinical impact and supporting a decision-making process for reporting was established.

Results: We identified SFs with high/moderate evidence of pathogenicity in 7.0% (27/383) of analyzed subjects. Among these, 12/27 (44.4%) were carriers of a high-risk recessive disease allele. The most represented disease domains were cancer predisposition (33.3%), cardiac disorders (16.7%), and familial hypercholesterolemia (12.5%).

Conclusion: Although still debated, ensuring during NGS-based genetic testing an opportunistic screening might be valuable for personal and familial early management and surveillance of medically actionable disorders, the individual’s reproductive choices, and the prevalence assessment of underestimated hereditary genetic diseases.

Newborn screening for genetic disorders: Current status and prospects for the future

Newborn screening (NBS) is a public health service aimed at identifying infants with severe genetic disorders, thus providing effective treatment early enough to prevent or ameliorate the onset of symptoms. Current NBS uses biochemical analysis of dried blood spots, predominately with time-resolved fluorescence immunoassay and tandem mass spectrometry, which produces some false positives and false negatives. The application of enzymatic activity-based testing technology provides a reliable screening method for some disorders. Genetic testing is now commonly used for secondary or confirmatory testing after a positive result in some NBS programs. Recently, next-generation sequencing (NGS) has emerged as a robust tool that enables large panels of genes to be scanned together rapidly. Rapid advances in NGS emphasize the potential for genomic sequencing to improve NBS programs. However, some challenges still remain and require solution before this is applied for population screening.

Application of next-generation sequencing in the diagnosis of gastric cancer

Objectives: Gastric cancer (GC) is a disease with high mortality, poor prognosis and numerous risk factors. GC has an asymptomatic nature in early stages of the diseases, making timely diagnosis complicated using common conventional approaches, namely pathological examinations and imaging tests. Recently, molecular profiling of GC using next generation sequencing (NGS) has opened new doors to efficient prognostic, diagnostic, and therapeutic strategies. The current review aims to thoroughly discuss and compare the current NGS techniques and commercial platforms utilized for GC diagnosis and treatment, highlighting the most recent NGS-based GC studies. Furthermore, this review addresses the challenges of clinical implementation of NGS in GC.Materials and methods: This review was conducted according to the eligible studies identified via search of Web of Science, PubMed, Scopus, Embase and the Cochrane Library. In the present study, data on gastric cancer patients and NGS methods used to diagnose the disease were reviewed.Conclusion: Given the ever-rising advancements in NGS technologies, bioinformatics, healthcare guidelines and refined classifications, it is hoped that these technologies can actualize their advantages and optimize GC patients' experience.

Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria

Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.

[Autoinflammation-A clinical and genetic challenge]

In the last two decades clinical rheumatological practice has been confronted with a steadily increasing number of autoinflammatory diseases, the immunological pathomechanisms of which have been elucidated and in part can be clinically well classified. Whereas targeted genetic diagnostics previously served to confirm a clinically suspected diagnosis, genetic sequencing technology has much improved and enables a new diagnostic approach via high-throughput sequencing, e.g., panel sequencing, whole exome and whole genome sequencing. Thus, the decision to make a diagnosis clinically and/or genetically, has become a daily challenge. This article contrasts the clinical, immunological and genetic aspects of autoinflammatory diseases.

A comprehensive WGS-based pipeline for the identification of new candidate genes in inherited retinal dystrophies

To enhance the use of Whole Genome Sequencing (WGS) in clinical practice, it is still necessary to standardize data analysis pipelines. Herein, we aimed to define a WGS-based algorithm for the accurate interpretation of variants in inherited retinal dystrophies (IRD). This study comprised 429 phenotyped individuals divided into three cohorts. A comparison of 14 pathogenicity predictors, and the re-definition of its cutoffs, were performed using panel-sequencing curated data from 209 genetically diagnosed individuals with IRD (training cohort). The optimal tool combinations, previously validated in 50 additional IRD individuals, were also tested in patients with hereditary cancer (n = 109), and with neurological diseases (n = 47) to evaluate the translational value of this approach (validation cohort). Then, our workflow was applied for the WGS-data analysis of 14 individuals from genetically undiagnosed IRD families (discovery cohort). The statistical analysis showed that the optimal filtering combination included CADDv1.6, MAPP, Grantham, and SIFT tools. Our pipeline allowed the identification of one homozygous variant in the candidate gene CFAP20 (c.337 C > T; p.Arg113Trp), a conserved ciliary gene, which was abundantly expressed in human retina and was located in the photoreceptors layer. Although further studies are needed, we propose CFAP20 as a candidate gene for autosomal recessive retinitis pigmentosa. Moreover, we offer a translational strategy for accurate WGS-data prioritization, which is essential for the advancement of personalized medicine.

A framework for reporting secondary and incidental findings in prenatal sequencing: When and for whom?

As the use of genomic sequencing (GS) in the prenatal setting becomes more widespread, laboratories and clinicians will be tasked with making decisions about whether to offer incidental and secondary findings to expectant parents and, if so, which ones. Unfortunately, few guidelines or position statements issued by professional bodies address the return of secondary findings specifically in the context of prenatal GS, nor do they offer clear guidance on whether, and which types of incidental findings should be reported. Laboratories and clinicians will also need to navigate other challenges, such as how to obtain sufficiently informed consent, workload burdens for both laboratories and clinicians, and funding. Here we discuss these, and other challenges associated with offering incidental and secondary findings in the context of prenatal GS. We outline existing guidelines for return of these findings, prenatally and in children. We review the existing literature on stakeholder perspectives on return of incidental and secondary findings and discuss the main practical and ethical challenges that require consideration. We then propose a framework to help guide decision-making, suggesting a baseline routine analysis, with additional layers of analysis that could be offered, according to local laboratory policy, with additional opt-in consent from the parents.

A systematic approach to the disclosure of genomic findings in clinical practice and research: a proposed framework with colored matrix and decision-making pathways

Background

Whether and how to disclose genomic findings obtained in the course of genomic clinical practice and medical research has been a controversial global bioethical issue over the past two decades. Although several recommendations and judgment tools for the disclosure of genomic findings have been proposed, none are sufficiently systematic or inclusive or even consistent with each other. In order to approach the disclosure/non-disclosure practice in an ethical manner, optimal and easy-to-use tools for supporting the judgment of physicians/researchers in genomic medicine are necessary.

Methods

The bioethics literature on this topic was analyzed to parse and deconstruct the somewhat overlapping and therefore ill-defined key concepts of genomic findings, such as incidental, primary, secondary, and other findings. Based on the deconstruction and conceptual analyses of these findings, we then defined key parameters from which to identify the strength of duty to disclose (SDD) for a genomic finding. These analyses were then applied to develop a framework with the SDD matrix and systematic decision-making pathways for the disclosure of genomic findings.

Results

The following six major parameters (axes), along with sub-axes, were identified: Axis 1 (settings and institutions where findings emerge); Axis 2 (presence or absence of intention and anticipatability in discovery); Axis 3 (maximal actionability at the time of discovery); Axis 4 (net medical importance); Axis 5 (expertise of treating physician/researcher); and Axis 6 (preferences of individual patients/research subjects for disclosure). For Axes 1 to 4, a colored SDD matrix for genomic findings was developed in which levels of obligation for disclosing a finding can be categorized. For Axes 5 and 6, systematic decision-making pathways were developed via the SDD matrix.

Conclusion

We analyzed the SDD of genomic findings and developed subsequent systematic decision-making pathways of whether and how to disclose genomic findings to patients/research subjects and their relatives in an ethical manner. Our comprehensive framework may help physicians and researchers in genomic medicine make consistent ethical judgments regarding the disclosure of genomic findings.

It takes guts to learn: machine learning techniques for disease detection from the gut microbiome

Associations between the human gut microbiome and expression of host illness have been noted in a variety of conditions ranging from gastrointestinal dysfunctions to neurological deficits. Machine learning (ML) methods have generated promising results for disease prediction from gut metagenomic information for diseases including liver cirrhosis and irritable bowel disease, but have lacked efficacy when predicting other illnesses. Here, we review current ML methods designed for disease classification from microbiome data. We highlight the computational challenges these methods have effectively overcome and discuss the biological components that have been overlooked to offer perspectives on future work in this area.

Biobanking and risk assessment: a comprehensive typology of risks for an adaptive risk governance

Biobanks act as the custodians for the access to and  responsible use of human biological samples and related data that have been generously donated by individuals to serve the public interest and scientific advances in the health research realm. Risk assessment has become a daily practice for biobanks and has been discussed from different perspectives. This paper aims to provide a literature review on risk assessment in order to put together a comprehensive typology of diverse risks biobanks could potentially face. Methodologically set as a typology, the conceptual approach used in this paper is based on the interdisciplinary analysis of scientific literature, the relevant ethical and legal instruments and practices in biobanking to identify how risks are assessed, considered and mitigated. Through an interdisciplinary mapping exercise, we have produced a typology of potential risks in biobanking, taking into consideration the perspectives of different stakeholders, such as institutional actors and publics, including participants and representative organizations. With this approach, we have identified the following risk types: economic, infrastructural, institutional, research community risks and participant's risks. The paper concludes by highlighting the necessity of an adaptive risk governance as an integral part of good governance in biobanking. In this regard, it contributes to sustainability in biobanking by assisting in the design of relevant risk management practices, where they are not already in place or require an update. The typology is intended to be useful from the early stages of establishing such a complex and multileveled biomedical infrastructure as well as to provide a catalogue of risks for improving the risk management practices already in place.

How to deal with uncertainty in prenatal genomics: A systematic review of guidelines and policies

Exome sequencing (ES) enhanced the diagnostic yield of genetic testing, but has also increased the possibility of uncertain findings. Prenatal ES is increasingly being offered after a fetal abnormality is detected through ultrasound. It is important to know how to handle uncertainty in this particularly stressful period. This systematic review aimed to provide a comprehensive overview of guidelines available for addressing uncertainty related to prenatal chromosomal microarray (CMA) and ES. Ten uncertainty types associated with prenatal ES and CMA were identified and defined by an international multidisciplinary team. Medline (all) and Embase were systematically searched. Laboratory scientists, clinical geneticists, psychologists, and a fetal medicine specialist screened the papers and performed the data extraction. Nineteen papers were included. Recommendations generally emphasized the importance of trio analysis, clinical information, data sharing, validation and re-analysis, protocols, multidisciplinary teams, genetic counselling, whether to limit the possible scope of results, and when to report particular findings. This systematic review helps provide a vocabulary for uncertainties, and a compass to navigate uncertainties. Prenatal CMA and ES guidelines provide a strong starting point for determining how to handle uncertainty. Gaps in guidelines and recommendations were identified and discussed to provide direction for future research and policy making.

Imagining genomic medicine futures in primary care: General practitioners' views on mainstreaming genomics in the National Health Service

Genomic medicine has captured the imaginations of policymakers and medical scientists keen to harness its health and economic potentials. In 2012, the UK government launched the 100,000 Genomes Project to sequence the genomes of British National Health Service (NHS) patients, laying the ground for mainstreaming genomic medicine in the NHS and developing the UK's genomics industry. However, the recent research and reports from national bodies monitoring genomic medicine's roll-out suggest both ethical and practical challenges for health-care professionals. Against this backdrop, this paper, drawing on qualitative research interviews with general practitioners (GPs) and documentary analysis of policy, explores GPs' views on mainstreaming genomic medicine in the NHS and implications for their practice. Analysing the NHS's genomic medicine agenda as a 'sociotechnical imaginary', we demonstrate that whilst sociotechnical imaginaries are construed as collectively shared understandings of the future, official visions of genomic medicine diverge from those at the forefront of health-care service delivery. Whilst policy discourse evokes hope and transformation of health care, some GPs see technology in formation, an unattainable 'utopia', with no relevance to their everyday clinical practice. Finding space for genomics requires bridging the gap between 'work as imagined' at the policy level and 'work as done' in health-care delivery.

Controlling my genome with my smartphone: first clinical experiences of the PROMISE system

Background

The development of Precision Medicine strategies requires high-dimensional phenotypic and genomic data, both of which are highly privacy-sensitive data types. Conventional data management systems lack the capabilities to sufficiently handle the expected large quantities of such sensitive data in a secure manner. PROMISE is a genetic data management concept that implements a highly secure platform for data exchange while preserving patient interests, privacy, and autonomy.

Methods

The concept of PROMISE to democratize genetic data was developed by an interdisciplinary team. It integrates a sophisticated cryptographic concept that allows only the patient to grant selective access to defined parts of his genetic information with single DNA base-pair resolution cryptography. The PROMISE system was developed for research purposes to evaluate the concept in a pilot study with nineteen cardiomyopathy patients undergoing genotyping, questionnaires, and longitudinal follow-up.

Results

The safety of genetic data was very important to 79%, and patients generally regarded the data as highly sensitive. More than half the patients reported that their attitude towards the handling of genetic data has changed after using the PROMISE app for 4 months (median). The patients reported higher confidence in data security and willingness to share their data with commercial third parties, including pharmaceutical companies (increase from 5 to 32%).

Conclusion

PROMISE democratizes genomic data by a transparent, secure, and patient-centric approach. This clinical pilot study evaluating a genetic data infrastructure is unique and shows that patient’s acceptance of data sharing can be increased by patient-centric decision-making.

Graphic abstract

Revisiting Secondary Information Related to Pharmacogenetic Testing

Incidental or secondary findings have been a major part of the discussion of genomic medicine research and clinical applications. For pharmacogenetic (PGx) testing, secondary findings arise due to the pleiotropic effects of pharmacogenes, often related to their endogenous functions. Unlike the guidelines that have been developed for whole exome or genome sequencing applications for management of secondary findings (though slightly different from PGx testing in that these refer to detection of variants in multiple genes, some with clinical significance and actionability), no corresponding guidelines have been developed for PGx clinical laboratories. Nonetheless, patient and provider education will remain key components of any PGx testing program to minimize adverse responses related to secondary findings.