P–546 Exome sequencing and preimplantation genetic testing for unexplained recurrent fetal malformations

Abstract Study question Could patient suffering unexplained recurrent fetal malformations be benefit of PGT-M by exome sequencing mutations identification? Summary answer Patients suffering unexplained recurrent fetal malformations could be benefit of the use of exome sequencing in combination to PGT-M to have a healthy live birth. What is known already Fetal malformations account for approximately 3% of live births and causes include: chromosomal abnormalities, exposure to toxic substances or teratogens and infections. Recently, studies have shown that several monogenic diseases are linked to fetal abnormalities. However, because of the large number of potential genes, genetic testing is challenging. Exome sequencing is widely used to detect genetic mutations and has emerged as a useful tool for finding the genetic cause of fetal abnormalities. The aim of this study was to show how exome sequencing in patients suffering unexplained recurrent fetal malformations in combination to PGT-M could lead to successful healthy newborn. Study design, size, duration Case report of a non-consanguineous couple with unexplained, recurrent fetal malformations. Couple were recruited during clinical consultation for unexplained recurrent fetal malformations at a private reproductive medicine clinic. The couple had two malformed fetus with the same congenital abnormalities: hydrocephalus, cerebellar vermis agenesis, cerebellar hypoplasia and enlarged cisterna magna. Patients signed written informed consent regarding to exome testing. For fetal sample, informed consent was obtained from parents. Participants/materials, setting, methods Sample of the affected fetus were provided. Parental genomic DNA was extracted from peripheral blood. Exome sequencing was performed using TrusightOne (Illumina®). FASTAQ data were processed through BWA and GATK algorithm. VCF files were analysed using Variant Interpreter software. After genetic counselling, PGT-M was performed using linkage polymorphic markers analysis and mutation sequencing. Embryo biopsy was carried at blastocyst stage. Embryos were vitrified and one healthy embryo was thaw and transfer in a subsequent cycle. Main results and the role of chance An homozygous novel pathogenic mutation c.641 C>T (p.Ala214Val) in FVLCR2 gene was found. The parents were heterozygous carriers revealing that the detected variant follow an autosomal recessive pattern. The FLVCR2 (14q24.3) gene encodes a transmembrane protein that belongs to the major facilitator superfamily of secondary carriers that transport small solutes in response to chemiosmosis ion gradients, such as calcium. Mutations in this gene are related to fetal central nervous system defects. This disorder is diagnosed prenatally and is lethal. PGT-M was recommended during genetic counselling. After control ovarian stimulation 14 oocytes were retrieved and finally 4 embryos were suitable for embryo biopsy at blastocyst stage. One embryo was diagnosed as healthy, two affected and one heterozygous carrier. The healthy embryo was thaw and transferred and a healthy male baby was born. Limitations, reasons for caution Exome sequencing has technical limitations: only covers mutations in coding regions and does not cover noncoding regions of the genome. It also cannot reliably detect copy-number variants at single gene level. Wider implications of the findings: This study offers strong evidence of exome-sequencing as a new diagnostic strategy and powerful tool discovering the underlying etiology of recurrent fetal malformations and identifying new genes important for human development. Using this strategy in combination with PGT-M, clinicians can help couples with recurrent fetal malformations to have healthy newborns. Trial registration number Not applicable

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Frequency and characterization of mutations in genes in a large cohort of patients referred to MODY registry

Journal of Pediatric Endocrinology and Metabolism ◽

10.1515/jpem-2020-0501 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Emily Breidbart ◽

Liyong Deng ◽

Patricia Lanzano ◽

Xiao Fan ◽

Jiancheng Guo ◽

...

Keyword(s):

Genetic Testing ◽

Exome Sequencing ◽

Large Scale ◽

Age Of Onset ◽

Family Members ◽

Ethnically Diverse ◽

Monogenic Diabetes ◽

Diabetes Diagnosis ◽

Pathogenic Variants ◽

Atypical Diabetes

Abstract Objectives There have been few large-scale studies utilizing exome sequencing for genetically undiagnosed maturity onset diabetes of the young (MODY), a monogenic form of diabetes that is under-recognized. We describe a cohort of 160 individuals with suspected monogenic diabetes who were genetically assessed for mutations in genes known to cause MODY. Methods We used a tiered testing approach focusing initially on GCK and HNF1A and then expanding to exome sequencing for those individuals without identified mutations in GCK or HNF1A. The average age of onset of hyperglycemia or diabetes diagnosis was 19 years (median 14 years) with an average HbA1C of 7.1%. Results Sixty (37.5%) probands had heterozygous likely pathogenic/pathogenic variants in one of the MODY genes, 90% of which were in GCK or HNF1A. Less frequently, mutations were identified in PDX1, HNF4A, HNF1B, and KCNJ11. For those probands with available family members, 100% of the variants segregated with diabetes in the family. Cascade genetic testing in families identified 75 additional family members with a familial MODY mutation. Conclusions Our study is one of the largest and most ethnically diverse studies using exome sequencing to assess MODY genes. Tiered testing is an effective strategy to genetically diagnose atypical diabetes, and familial cascade genetic testing identified on average one additional family member with monogenic diabetes for each mutation identified in a proband.

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Health system interventions to integrate genetic testing in routine oncology services: A systematic review

PLoS ONE ◽

10.1371/journal.pone.0250379 ◽

2021 ◽

Vol 16 (5) ◽

pp. e0250379

Author(s):

Rosie O’Shea ◽

Natalie Taylor ◽

Ashley Crook ◽

Chris Jacobs ◽

Yoon Jung Kang ◽

...

Keyword(s):

Systematic Review ◽

Genetic Testing ◽

Genetic Counselling ◽

Implementation Research ◽

Professional Education ◽

Data Extraction ◽

Complex Interventions ◽

Implementation Strategies ◽

Newcastle Ottawa Scale ◽

Inner Setting

Background Integration of genetic testing into routine oncology care could improve access to testing. This systematic review investigated interventions and the tailored implementation strategies aimed at increasing access to genetic counselling and testing and identifying hereditary cancer in oncology. Methods The search strategy results were reported using the PRISMA statement and four electronic databases were searched. Eligible studies included routine genetic testing for breast and ovarian cancer or uptake after universal tumour screening for colorectal or endometrial cancer. The titles and abstracts were reviewed and the full text articles screened for eligibility. Data extraction was preformed using a designed template and study appraisal was assessed using an adapted Newcastle Ottawa Scale. Extracted data were mapped to Proctor’s et al outcomes and the Consolidated Framework for Implementation Research and qualitatively synthesised. Results Twenty-seven studies, published up to May 2020, met the inclusion criteria. Twenty-five studies ranged from poor (72%), fair to good (28%) quality. Most interventions identified were complex (multiple components) such as; patient or health professional education, interdisciplinary practice and a documentation or system change. Forty-eight percent of studies with complex interventions demonstrated on average a 35% increase in access to genetic counselling and a 15% increase in testing completion. Mapping of study outcomes showed that 70% and 32% of the studies aligned with either the service and client or the implementation level outcome and 96% to the process or inner setting domains of the Consolidated Framework for Implementation Research. Conclusion Existing evidence suggests that complex interventions have a potentially positive effect towards genetic counselling and testing completion rates in oncology services. Studies of sound methodological quality that explore a greater breadth of pre and post implementation outcomes and informed by theory are needed. Such research could inform future service delivery models for the integration of genetics into oncology services.

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Short Tandem Repeats Used in Preimplantation Genetic Testing of Β-Thalassemia: Genetic Polymorphisms For 15 Linked Loci in the Vietnamese Population

Open Access Macedonian Journal of Medical Sciences ◽

10.3889/oamjms.2019.840 ◽

2019 ◽

Vol 7 (24) ◽

pp. 4383-4388

Author(s):

Dang Tien Truong ◽

Ngo Van Nhat Minh ◽

Dinh Phuong Nhung ◽

Hoang Van Luong ◽

Do Quyet ◽

...

Keyword(s):

At Risk ◽

Genetic Testing ◽

Tandem Repeats ◽

Drop Out ◽

Preimplantation Genetic Testing ◽

Thalassemia Patient ◽

Gene Assay ◽

Monogenic Diseases ◽

Vietnamese Population ◽

Short Tandem

BACKGROUND: β-thalassemia is one of the most common monogenic diseases worldwide. Preimplantation genetic testing (PGT) of β-thalassemia is performed to avoid affected pregnancies has become increasingly popular worldwide. In which, the indirect analysis using short tandem repeat (STRs) linking with HBB gene to detect different β-globin (HBB) gene mutation is a simple, accurate, economical and also provides additional control of contamination and allele-drop-out ADO. AIM: This study established microsatellite markers for PGT of Vietnamese β-thalassemia patient. METHODS: Fifteen (15) STRs gathered from 5 populations were identified by in silico tools within 1 Mb flanking the HBB gene. The multiplex PCR reaction was optimized and performed on 106 DNA samples from at-risk families. RESULTS: After estimating, PIC values were ≥ 0.7 for all markers, with expected heterozygosity and observed heterozygosity values ranged from 0.81 to 0.92 and 0.53 to 0.86, respectively. One hundred percent of individuals had at least seven heterozygous markers and were found to be heterozygous for at least two markers on either side of the HBB gene. The STRs panel was successfully performed on one at-risk family. CONCLUSION: In general, a pentadecaplex marker (all < 1 Mb from the HBB gene) assay was constituted for β-thalassemia PGT on Vietnamese population.

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Whole-Exome Sequencing Analysis of Human Semen Quality in Russian Multiethnic Population

Frontiers in Genetics ◽

10.3389/fgene.2021.662846 ◽

2021 ◽

Vol 12 ◽

Author(s):

Semyon Kolmykov ◽

Gennady Vasiliev ◽

Ludmila Osadchuk ◽

Maxim Kleschev ◽

Alexander Osadchuk

Keyword(s):

Exome Sequencing ◽

Ethnic Groups ◽

Whole Exome Sequencing ◽

Complex Traits ◽

Semen Quality ◽

Population Sample ◽

Sperm Concentration ◽

Sequencing Analysis ◽

New Genes ◽

Whole Exome

The global trend toward the reduction of human spermatogenic function observed in many countries, including Russia, raised the problem of extensive screening and monitoring of male fertility and elucidation of its genetic and ethnic mechanisms. Recently, whole-exome sequencing (WES) was developed as a powerful tool for genetic analysis of complex traits. We present here the first Russian WES study for identification of new genes associated with semen quality. The experimental 3 × 2 design of the WES study was based on the analysis of 157 samples including three ethnic groups—Slavs (59), Buryats (n = 49), and Yakuts (n = 49), and two different semen quality groups—pathozoospermia (n = 95) and normospermia (n = 62). Additionally, our WES study group was negative for complete AZF microdeletions of the Y-chromosome. The normospermia group included men with normal sperm parameters in accordance with the WHO-recommended reference limit. The pathozoospermia group included men with impaired semen quality, namely, with any combined parameters of sperm concentration <15 × 106/ml, and/or progressive motility <32%, and/or normal morphology <4%. The WES was performed for all 157 samples. Subsequent calling and filtering of variants were carried out according to the GATK Best Practices recommendations. On the genotyping stage, the samples were combined into four cohorts: three sets corresponded to three ethnic groups, and the fourth set contained all the 157 whole-exome samples. Association of the obtained polymorphisms with semen quality parameters was investigated using the χ2 test. To prioritize the obtained variants associated with pathozoospermia, their effects were determined using Ensembl Variant Effect Predictor. Moreover, polymorphisms located in genes expressed in the testis were revealed based on the genomic annotation. As a result, the nine potential SNP markers rs6971091, rs557806, rs610308, rs556052, rs1289658, rs278981, rs1129172, rs12268007, and rs17228441 were selected for subsequent verification on our previously collected population sample (about 1,500 males). The selected variants located in seven genes FAM71F1, PPP1R15A, TRIM45, PRAME, RBM47, WDFY4, and FSIP2 that are expressed in the testis and play an important role in cell proliferation, meiosis, and apoptosis.

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Audit of the Aetiological Investigations Performed in Children with Sensorineural Hearing Loss At Salford

Manchester Medical Journal ◽

10.7227/mmj.0031 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Saud K AlHajeri ◽

Dr Mohammed Iqbal

Keyword(s):

Hearing Loss ◽

Genetic Testing ◽

Sensorineural Hearing Loss ◽

Genetic Counselling ◽

Gold Standard ◽

Sensorineural Hearing ◽

British Association ◽

Hearing Tests ◽

Work Up

Objective: This project aims to look at the Audiovestibular Physician’s practice at Salford and how closely it aligns with the gold standard guidelines set in the protocol lately published by the British Association of Audiological Physicians. Method: An audit was done retrospectively on 20 patients suffering from sensorineural hearing loss. As such, patient notes were utilised to ascertain which aetiological investigations have been completed and which were not. Any inadequacy in the aetiological work up has been dissected to help know the underlying reasons. Results: All patients had a thorough history taken and were comprehensively physically examined. 95% of patients underwent imaging in the form of MRI/CT. 80% received CMV testing. 75% underwent ECG testing. 60% received family hearing tests. Only 35% had ophthalmology examinations and 25% underwent urine and genetic testing. Conclusion: In some cases, the low compliance rates were due to the Audiovestibular Physician not ordering the investigation as part of the aetiological work up. This could be improved with the use of a dedicated checklist to act as an aid to the physician. Moreover, genetic counselling has been proposed to attempt to boost the compliance rates with genetic testing and similarly, leaflets briefing patients’ families about the importance of undergoing hearing tests themselves is another promising proposition to help improve the adherence

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American Society of Clinical Oncology Policy Statement Update: Genetic Testing for Cancer Susceptibility

Journal of Clinical Oncology ◽

10.1200/jco.2003.03.189 ◽

2003 ◽

Vol 21 (12) ◽

pp. 2397-2406 ◽

Cited By ~ 516

Keyword(s):

Genetic Testing ◽

Informed Consent ◽

Hereditary Cancer ◽

Cancer Susceptibility ◽

Cancer Genetics ◽

Family Members ◽

Educational Opportunities ◽

Increased Risk ◽

Post Test ◽

Risk Of Cancer

Executive Summary: As the leading organization representing cancer specialists involved in patient care and clinical research, the American Society of Clinical Oncology (ASCO) reaffirms its commitment to integrating cancer risk assessment and management, including molecular analysis of cancer predisposition genes, into the practice of oncology and preventive medicine. The primary goal of this effort is to foster expanded access to, and continued advances in, medical care provided to patients and families affected by hereditary cancer syndromes. The 1996 ASCO Statement on Genetic Testing for Cancer Susceptibility set forth specific recommendations relating to clinical practice, research needs, educational opportunities, requirement for informed consent, indications for genetic testing, regulation of laboratories, and protection from discrimination, as well as access to and reimbursement for cancer genetics services. In updating this Statement, ASCO endorses the following principles: Indications for Genetic Testing:ASCO recommends that genetic testing be offered when 1) the individual has personal or family history features suggestive of a genetic cancer susceptibility condition, 2) the test can be adequately interpreted, and 3) the results will aid in diagnosis or influence the medical or surgical management of the patient or family members at hereditary risk of cancer. ASCO recommends that genetic testing only be done in the setting of pre- and post-test counseling, which should include discussion of possible risks and benefits of cancer early detection and prevention modalities. Special Issues in Testing Children for Cancer Susceptibility:ASCO recommends that the decision to offer testing to potentially affected children should take into account the availability of evidence-based risk-reduction strategies and the probability of developing a malignancy during childhood. Where risk-reduction strategies are available or cancer predominantly develops in childhood, ASCO believes that the scope of parental authority encompasses the right to decide for or against testing. In the absence of increased risk of a childhood malignancy, ASCO recommends delaying genetic testing until an individual is of sufficient age to make an informed decision regarding such tests. As in other areas of pediatric care, the clinical cancer genetics professional should be an advocate for the best interests of the child. Counseling About Medical Management After Testing:ASCO recommends that oncologists include in pre- and post-test counseling the discussion of possible risks and benefits of cancer early-detection and prevention modalities, some of which have presumed but unproven efficacy for individuals at increased hereditary risk of cancer. Regulation of Genetic Testing:ASCO recommends strengthening regulatory oversight of laboratories that provide clinical cancer predisposition tests. These quality assurance mechanisms should include oversight of the reagents used in genetic testing, interlaboratory comparisons of reference samples, standardization of laboratory genetic test reports, and proficiency testing. Protection From Insurance and Employment Discrimination:ASCO supports establishing a federal law to prohibit discrimination by health insurance providers and employers on the basis of an individual’s inherited susceptibility to cancer. Protections against genetic discrimination should apply to those with group coverage, those with individual health insurance policies, and the uninsured. Coverage of Services:ASCO supports efforts to ensure that all individuals at significantly increased risk of hereditary cancer have access to appropriate genetic counseling, testing, screening, surveillance, and all related medical and surgical interventions, which should be covered without penalty by public and private third-party payers. Confidentiality and Communication of Familial Risk:ASCO recommends that providers make concerted efforts to protect the confidentiality of genetic information. However, they should remind patients of the importance of communicating test results to family members, as part of pretest counseling and informed consent discussions. ASCO believes that the cancer care provider’s obligations (if any) to at-risk relatives are best fulfilled by communication of familial risk to the person undergoing testing, emphasizing the importance of sharing this information with family members so that they may also benefit. Educational Opportunities in Genetics:ASCO is committed to continuing to provide educational opportunities for physicians and other health care providers regarding the methods of cancer risk assessment, the clinical characteristics of hereditary cancer susceptibility syndromes, and the range of issues related to genetic testing, including pre- and post-test genetic counseling, and risk management, so that health professionals may responsibly integrate the care of persons at increased genetic risk of cancer into the practice of clinical and preventive oncology. Special Issues Relating to Genetic Research on Human Tissues:ASCO recommends that all researchers proposing to use or store human biologic specimens for genetic studies should consult either the responsible institutional review board (IRB) or a comparable body specifically constituted to assess human tissue research, to determine the requirements for protection specific to the study under consideration. This consultation should take place before the project is initiated. The determination of the need for informed consent or authorization in such studies should depend on whether the research involves tests for genetic markers of known clinical significance and whether research data will be linked to protected health information, as well as other considerations specific to the study proposed. Special attention should also be paid to 1) whether future research findings will be disclosed to the research participants, 2) whether future contact of participants is planned, 3) whether and how protected health information about the tissue donors will be stored, and what will happen to study specimens after the trial ends. In addition, ASCO affirms the right of people contributing tissue to a databank to rescind their permission, in accordance with federal privacy regulations.

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Abstract 16468: Results of Research Genetic Testing in Pediatric Cardiomyopathy Patients Justify Broader Clinical Genetic Testing

Circulation ◽

10.1161/circ.132.suppl_3.16468 ◽

2015 ◽

Vol 132 (suppl_3) ◽

Author(s):

Stephanie M Ware ◽

Steven E Lipshultz ◽

Steven D Colan ◽

Ling Shi ◽

Charles E Canter ◽

...

Keyword(s):

Genetic Testing ◽

Family History ◽

Risk Stratification ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Clinical Genetic ◽

Clinical Genetic Testing ◽

Whole Exome ◽

Pediatric Cardiomyopathy ◽

History Of

Introduction: Pediatric cardiomyopathies are genetically heterogeneous diseases with high risk of death or cardiac transplant. Despite progress in identifying causes, the majority of cases remain idiopathic. Currrently, genetic testing is not performed in all children with cardiomyopathy. Gene identification leads to better individual risk stratification and has the potential to stimulate the development of therapies based on the underlying mutation. The aim of this study is to identify genetic mutations in pediatric cardiomyopathy patients using whole exome sequencing. Hypothesis: Sarcomeric mutations are under-diagnosed causes of all forms of cardiomyopathy in children. Methods: Probands with cardiomyopathy were recruited from 11 institutions. Results of clinical genetic testing prior to enrollment were collected. Whole exome sequencing was performed and mutations were identified in 35 genes currently available on clinical genetic testing panels. Results: The initial 154 probands subjected to exome included 78 patients with DCM, 43 with HCM, 14 with RCM, and 19 with LVNC, mixed, or unknown types. Familial disease was present in 38% and the remainder were idiopathic. Twenty-seven percent had positive clinical genetic testing prior to enrollment. Exome testing identified mutations in 38 subjects who had not had clinical testing, increasing the cohort positive testing rate to 55% (DCM, 34.6%; HCM, 74.4%; RCM, 71.4%). Forty-five percent of subjects with no family history of disease had an identifiable mutation. Conclusions: Pediatric cardiomyopathy patients have a high incidence of mutations that can be identified by clinically available genetic testing. Lack of a family history of cardiomyopathy was not predictive of normal genetic testing. These results support the broader use of genetic testing in pediatric patients with all functional phenotypes of cardiomyopathy to identify disease causation allowing better family risk stratification.

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Exome Sequencing Reveals De Novo Variants in Congenital Scoliosis

Journal of Pediatric Genetics ◽

10.1055/s-0041-1726282 ◽

2021 ◽

Author(s):

Kohei Murakami ◽

Shingo Kikugawa ◽

Shoji Seki ◽

Hidetomi Terai ◽

Takako Suzuki ◽

...

Keyword(s):

Exome Sequencing ◽

Disease Susceptibility ◽

De Novo ◽

Congenital Scoliosis ◽

Japanese Patients ◽

Variant Interpretation ◽

Functional Studies ◽

New Genes ◽

Lateral Curvature ◽

Vertebral Anomalies

AbstractCongenital scoliosis (CS) is a lateral curvature of the spine characterized by the presence of vertebral anomalies. Pathogenic genetic variants in the TBX6 gene are one of the causes of CS. However, since many clinically diagnosed cases of CS are without known TBX6 gene variations, this study aims to uncover new genes related to disease susceptibility of CS by exome sequencing (ES). This study employed ES in a cohort of 5 Japanese patients with CS and their healthy parents or a sister for a total of 16 samples among 5 families. Variant interpretation was performed using SIFT, PolyPhen-2, Mutation Taster, and CADD. Four de novo variants were identified by ES and confirmed by Sanger sequencing: 1 frameshift variant (SHISA3) and 3 missense variants (AGBL5, HDAC4, and PDE2A). ES also uncovered 1 homozygous variant in the MOCOS gene. All of these variants were predicted to be deleterious by SIFT, PolyPhen-2, Mutation Taster, and/or CADD. The number of de novo variants identified in this study was exactly what would be expected by chance. Additional functional studies or gathering matched patients using Gene Matcher are needed.

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Preimplantation Genetics

Reproductive Ethics in Clinical Practice ◽

10.1093/med/9780190873028.003.0009 ◽

2021 ◽

pp. 98-109

Author(s):

Valerie Gutmann Koch

Keyword(s):

Genetic Testing ◽

Informed Consent ◽

Genetic Disease ◽

Chromosomal Abnormalities ◽

Preimplantation Genetic Testing ◽

Economic Implications ◽

Genetic Traits ◽

Ethical Implications ◽

Wrongful Life ◽

Wrongful Birth

This chapter highlights the uses and ethical implications of preimplantation genetic testing and addresses the topic of liability as it applies to use of this technology to screen and select embryos for chromosomal abnormalities and genetic traits prior to implantation. When errors or wrongs occur, there may be significant medical, psychological, and economic implications for those individuals who sought preimplantation testing to avoid a genetic disease or to improve the chance of achieving pregnancy. Informed consent, wrongful birth, and wrongful life claims may be available to those who are harmed due to these errors.

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