Implications of genetic testing and informed consent before and after genetic testing in individuals with cancer

Recent advancements in next generation sequencing have allowed for genetic information become more readily available in the clinical setting for those affected by cancer and by treating clinicians.Given the lack of access to geneticists,medical oncologists and other treating physicians have begun ordering and interpreting genetic tests for individuals with cancer through the process of"mainstreaming".While this process has allowed for quicker access to genetic tests,the process of"mainstreaming"has also brought several challenges including the dissemination of variants of unknown significance results,ordering of appropriate tests,and accurate interpretation of genetic results with appropriate followup testing and interventions.In this editorial,we seek to explore the process of informed consent of individuals before obtaining genetic testing and offer potential solutions to optimize the informed consent process including categorization of results as well as a layered consent model.

Advances of Genetic Testing Technology in Etiology Diagnosis of Recurrent Spontaneous Abortion

Recurrent spontaneous abortion (RSA) is a complex and heterogeneous disorder with multiple etiologies. Genetic factors are thought to play an important role in the etiology of RSA. With recent advances in genetic testing technologies, there has been an increasing interest in using these tools to diagnose the etiology of RSA. This review discusses the different types of genetic testing methods, such as karyotyping, chromosomal microarray analysis, next-generation sequencing, and their applications in the diagnosis of the etiology RSA. The use of genetic testing in the diagnosis of RSA has the potential to improve the accuracy of diagnosis and the understanding of the underlying mechanisms of the disorder, which could lead to better management and treatment of affected individuals.

Current scenario of the genetic testing for rare neurological disorders exploiting next generation sequencing

Next generation sequencing is currently a cornerstone of genetic testing in routine diagnostics,allowing for the detection of sequence variants with so far unprecedented large scale,mainly in genetically heterogenous diseases,such as neurological disorders.It is a fast-moving field,where new wet enrichment protocols and bioinformatics tools are constantly being developed to overcome initial limitations.Despite the as yet undiscussed advantages,however,there are still some challenges in data analysis and the interpretation of variants.In this review,we address the current state of next generation sequencing diagnostic testing for inherited human disorders,particularly giving an overview of the available high-throughput sequencing approaches;including targeted,whole-exome and whole-genome sequencing;and discussing the main critical aspects of the bioinformatic process,from raw data analysis to molecular diagnosis.

Clinicopathological analysis of early-stage breast cancer patients that meet indications for BRCA 1/2 genetic testing

Objective:To investigate the clinicopathological characteristics and prognostic factors of early-stage breast cancer patients with indications for breast cancer susceptibility genes 1/2(BRCA1/2)genetic testing in China.Methods:Based on the indication criteria for BRCA genetic testing specified in the National Comprehensive Cancer Network(NCCN)clinical practice guidelines in oncology,genetic/familial high-risk assessment:Breast and ovarian(Version 2.2019),a retrospective analysis was performed on patients with early-stage invasive breast cancer treated at Breast Disease Center,Peking University First Hospital between January 2008 and December 2016.Clinicopathological characteristics of all patients were analyzed,and prognoses were calculated using the KaplanMeier method and a Cox proportionate hazards model.Results:A total of 906 early-stage breast cancer patients who had indications for BRCA genetic testing and had complete clinicopathological data and follow-up information were included in the study group,accounting for34.7%of all breast cancer patients treated in Breast Disease Center,Peking University First Hospital during the study period.Compared with breast cancer patients without indications for BRCA genetic testing,the overall survival(OS)and disease-free survival(DFS)of patients with indications were not significantly different.In the study group,patients with premenopausal status,high T stage,lymph node positive,estrogen receptor(ER)negative,Ki-67>20%and presence of a vascular tumor thrombus had worse prognosis.There were more family histories of gastrointestinal cancer in patients with related indications than in patients without such indications.Conclusions:Single-center data showed that more than 30%of patients with early-stage breast cancer had indications for BRCA genetic testing.There was no prognostic difference in patients with or without indications for BRCA genetic testing.Premenopausal status,high T stage,lymph node positive,ER negative,Ki-67>20%,and presence of a vascular tumor thrombus were associated with poor prognosis.

2+0 CYP21A2 deletion carrier—a limitation of the genetic testing and counseling:A case report

BACKGROUND CYP21A2 gene mutations may all cause reduction or loss of 21-hydroxylase activity,leading to development of congenital adrenal hyperplasia(CAH)with different clinical phenotypes.For families with CAH children,genetic testing of the parents and genetic counseling are recommended to assess the risk of recurrence.CASE SUMMARY We report a case of CAH with a high suspicion before delivery.The risk of the child suffering from CAH during the pregnancy had been underestimated due to the deviation of genetic counseling and genetic testing results.Our report confirmed a CYP21A2 homozygous deletion in this case,CYP21A2 heterozygous deletion in the mother,and a rare 2+0 CYP21A2 deletion in the father.CONCLUSION It is important to analyze the distribution of CYP21A2 gene in the two alleles of parents of children with CAH.

Role of genetic testing in cardiomyopathies:Αprimer for cardiologists

Recent advances in cardiovascular genetics have transformed genetic testing into a valuable part of management of families with inherited cardiomyopathies.As novel mutations have been identified,understanding when to consider genetic testing has emerged as an important consideration in the management of these cases.Specific genetic testing has a paramount importance in the risk stratification of family members,in the prognosis of probands at higher risk of a serious phenotype expression,and finally in the identification of new mutations,all of which are discussed in this review.The indications for each type of cardiomyopathy are described,along with the limitations of genetic testing.Finally,the importance of public sharing of variants in large data sets is emphasized.The ultimate aim of this review is to present key messages about the genetic testing process in order to minimize potential harms and provide suggestions to specialized clinicians who act as a part of a multidisciplinary team in order to offer the best care to families with inherited cardiomyopathies.

Whole-genome amplification/preimplantation genetic testing for propionic acidemia of successful pregnancy in an obligate carrier Mexican couple:A case report

BACKGROUND Identifying a potential single monogenetic disorder in healthy couples is costly due to the Assisted Reproduction facilities'current methodology for screening,which focuses on the detecting multiple genetic disorders at once.Here,we report the successful application of a low-cost and fast preimplantation genetic testing for monogenic/single gene defects(PGT-M)approach for detecting propionic acidemia(PA)in embryos obtained from a confirmed heterozygous propionyl-CoA carboxylase alpha subunit(PCCA)couple.CASE SUMMARY A fertile 32-years old Mexican couple with denied consanguinity sought antenatal genetic counseling.They were suspected obligate PA carriers due to a previous deceased PA male newborn with an unknown PCCA/propionyl-CoA carboxylase beta subunit(PCCB)genotype.Next-Generation Sequencing revealed a heterozygous genotype for a pathogenic PCCA variant(c.2041-1G>T,ClinVar:RCV-000802701.1;dbSNP:rs1367867218)in both parents.The couple requested in vitro fertilization(IVF)and PGT-M for PA.From IVF,12 oocytes were collected and fertilized,of which two resulted in high-quality embryos.Trophectoderm biopsies and Whole Genome Amplification by a fragmentation/amplification-based method were performed and revealed that the two embryos were euploid.Endpoint polymerase chain reaction and further Sanger sequencing of the exon-intron borders revealed a wild-type PCCA male embryo and a heterozygous c.2041-1G>T female embryo.Both embryos were transferred,resulting in a clinical pregnancy and the delivery of a healthy male newborn(38 wk,weight:4080 g,length:49 cm,APGAR 9/9).The absence of PA was confirmed by expanded newborn screening.CONCLUSION We show that using PGT-M with Whole Genome Amplification templates,coupled with IVF,can reduce the transmission of a pathogenic variant of the PCCA gene.

Uncertainty following an inconclusive result from the BRCA1/2 genetic test:A review about psychological outcomes

BACKGROUND An inconclusive result from BRCA1/2 genetic testing indicates that a genetic variant of uncertain significance is detected.This case constitutes the majority of genetic test results,but studies specifically addressing the psychological adjustment of people with inconclusive results are scarce.AIM To examine psychological outcomes of receiving an uninformative BRCA1/2 test result.METHODS PubMed,PsychInfo,and Cochrane Central Register of Controlled Trials were screened for studies focusing on distress,anxiety,and depression levels in individuals with inconclusive genetic test results.This review is based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses method.RESULTS Studies on psychological outcomes of inconclusive BRCA1/2 focused on general and specific distress,anxiety,and depression.Overall,they produced mixed results.These inconsistent findings are probably due to the uncertainty caused by this type of result,that may also influence the decisions of individuals about surveillance and prophylactic options,reducing their compliance.In addition,this review highlights specific risk and protective factors that affect psychological adjustment in individuals with an inconclusive genetic testing result.CONCLUSION Individuals with inconclusive genetic test results need specific educational programs and support to better understand the meaning of their results in order to be able to make decisions about surveillance and prophylactic options.

Preimplantation genetic testing for embryos predisposed to hereditary cancer:Possibilities and challenges

Preimplantation genetic testing(PGT),which was developed as an alternative to prenatal genetic testing,allows couples to avoid pregnancies with abnormal chromosomes and the subsequent termination of the affected fetus.Originally used for early onset monogenic conditions,PGT is now used to prevent various types of inherited cancer conditions based on the development of PGT technology,assisted reproductive techniques(ARTs),and in vitro fertilization(IVF).This review provides insights into the potential benefits and challenges associated with the application of PGT for hereditary cancer and provides an overview of the existing literature on this test,with a particular focus on the current challenges related to laws,ethics,counseling,and technology.Additionally,this review predicts the future potential applications of this method.Although PGT may be utilized to predict and prevent hereditary cancer,each case should be comprehensively evaluated.The motives of couples must be assessed to prevent the misuse of this technique for eugenic purposes,and non-pathogenic phenotypes must be carefully evaluated.Pathological cases that require this technology should also be carefully considered based on legal and ethical reasoning.PGT may be the preferred treatment for hereditary cancer cases;however,such cases require careful case-by-case evaluations.Therefore,this study concludes that multidisciplinary counseling and support for patients and their families are essential to ensure that PGT is a viable option that meets all legal and ethical concerns.

A review of pre-implantation genetic testing technologies and applications

The first practice of pre-implantation genetic testing(PGT)was reported more than 30 years ago.PGT,originally named preimplantation genetic screening(PGS)and pre-implantation genetic diagnosis(PGD),is now categorized as PGT for aneuploidies(PGT-A),PGT for monogenic/single-gene defects(PGT-M),and PGT for chromosomal structural rearrangements(PGT-SR).Patients with fertility issues caused by advanced maternal age,carrier status of chromosomal abnormalities,or harboring pathogenic variant(s)are recommended to undergo PGT to increase the possibility of successful live birth and avoid potentially affected newborns.High-throughput techniques,such as DNA microarrays and next-generation sequencing(NGS),have enabled comprehensive screening of all 24 chromosomes,instead of few loci at a time.Furthermore,as a comprehensive PGT,PGT-Plus was enabled by the rapid development of a genome-wide single-cell haplotyping technique to detect embryo aneuploidy,single-gene disorders,and chromosomal aberrations simultaneously using a single universal protocol.In addition,non-invasive approaches enable a more intact embryo during the biopsy procedure,which may avoid potential mosaicism issues at a certain scale by testing spent culture media(SCM).As a novel PGT application,PGT-P detects genome-wide variations in polygenic diseases,which account for a large proportion of premature human deaths and affect a markedly larger population than monogenic diseases,using polygenic risk score calculation to decrease the potential of affecting complex conditions.Owing to the emergence of new technologies recruited to PGTs,more couples with infertility issues have a promising chance of conceiving a healthy baby,ultimately facilitating the human species to live more prosper.

Preimplantation genetic testing guidelines of International Society of Reproductive Genetics

The International Society of Reproductive Genetics(ISRG)assembled a workgroup made up of clinicians,clinical laboratory directors,and scientists for the purpose of creating the guidelines for preimplantation genetic testing(PGT).The most up-to-date information and clinical insights for the optimal PGT practice were incorporated in these guidelines.Recommendations are provided for embryologists,medical geneticists,clinical laboratorians,and other healthcare providers to improve the wellbeing of patients seeking assisted reproductive treatment and their offspring.

Preimplantation genetic testing for aneuploidy improves clinical outcomes in patients with repeated implantation failure

Objective:The objective of this study is to study whether preimplantation genetic testing for aneuploidy(PGT-A)improves the clinical outcomes of infertile patients with repeated implantation failure(RIF)undergoing frozen-thawed embryo transfer.Methods:This is a retrospective analysis of clinical pregnancy,live birth,miscarriage rates,and obstetric and perinatal outcomes of women with RIF with or without PGT-A.Statistical analyses of categorical data were performed using propensity score matching(PSM),χ^(2)test,and Student’s t test.Results:We enrolled 466 patients with RIF,of which,209 were in the RIF-PGT-A group.The rate of euploid blastocysts was significantly associated with age and day 5 or 6 blastocysts.There were significant differences between the RIF-PGT-A group and the RIF-non-PGT-A group across several parameters.After PSM,positive serum human chorionic gonadotropin(56.9%and 33.9%,P<0.01),clinical pregnancy(49.5%and 31.2%,P<0.01),live birth(43.1%and 25.7%,P<0.01),and fetal heart rates(50.0%and 29.8%,P<0.01)per transfer were significantly higher in the RIF-PGT-A group.Conclusion:Elective single-embryo transfer PGT-A can minimize the risk of obstetric and perinatal outcomes,especially fetal body weight,in women with RIF.Additionally,PGT-A can significantly improve pregnancy and live birth rates.

Retrospective Cohort Study of Preimplantation Genetic Testing for Aneuploidy with Comprehensive Chromosome Screening versus Nonpreimplantation Genetic Testing in Normal Karyotype,Secondary Infertility Patients with Recurrent Pregnancy Loss

Objective:To evaluate whether preimplantation genetic testing for aneuploidy(PGT-A)with comprehensive chromosome screening increases live birth rate(LBR)in normal karyotype couples with recurrent pregnancy loss(RPL).Methods:A retrospective cohort follow-up study of 506 couples with RPL was conducted between April 2014 and March 2017.Couples were allocated to two groups according to their decision to choose PGT-A or not.The primary outcome was LBR per start/transfer cycle;secondary outcomes were ongoing pregnancy rate and miscarriage rate.Statistical analyses were conducted using univariate and multivariate logistic regression models adjusted for maternal age.Results:LBR per start(26.6%vs.15.4%,relative risk[RR]:2.66,95%confidence interval[CI][1.69-4.20],P<0.0001;adjusted RR[aRR]:2.40,95%CI[1.49-3.86],P=0.0004)and per transfer(44.9%vs.25.1%,RR:3.00,95%CI[1.96-4.60],P<0.0001;aRR:2.64,95%CI[1.68-4.14],P<0.0001)was significantly higher in the PGT-A group than in the non-PGT-A group.The miscarriage rate was significantly lower in the PGT-A group compared to the non-PGT-A group(15.7%vs.34.6%,RR:0.27,95%CI[0.13-0.57],P=0.00005;aRR:0.26,95%CI[0.12-0.57],P=0.0007).Conclusions:LBR per start cycle following PGT-A is significantly higher,and risk of miscarriage is significantly lower among infertile couples with RPL,irrespective of maternal age.PGT-A should be recommended to infertile couples with RPL.

Noninvasive preimplantation genetic testing in assisted reproductive technology:current state and future perspectives

Invasive genetic screening of pre-implantation embryos via biopsied trophectoderm(TE)cells has been in use for more than 20 years,while its benefits in selecting euploid embryos remain controversial.Recent advances in the ability to process embryonic cell-free DNA(cfDNA)from blastocoel fluid(BF)and spent culture media(SCM)of blastocysts in a manner similar to that of a biopsied TE sample provide a potential alternative holding great promise for obtaining cytogenetic information of the embryos without intrusive biopsy of traditional biopsy-based pre-implantation genetic testing(PGT).Several studies have reported even higher diagnostic accuracy in non-invasive PGT(ni-PGT)than conventional PGT.However,there are still several technical challenges to be overcome before ni-PGT can be accepted as a reliable genomic information source of embryo.In this review,we have summarized the emergence and current state of ni-PGT,and discussed our own perspectives on their limitations and future prospect.There is still a long way to go before truly wide clinical application of ni-PGT.

Current Status and Recent Advances in Preimplantation Genetic Testing for Structural Rearrangements

Preimplantation genetic testing(PGT)is an early form of prenatal genetic diagnosis,which can identify the abnormal embryos cultured in vitro,allow only transfer of genetically normal embryos,and improve the pregnancy rate.In recent years,the rapid development of microarrays and next-generation sequencing(NGS)technologies has remarkably accelerated the clinical application of PGT.In particular,a variety of detection methods have emerged and achieved significant progress in PGT for structural rearrangements(PGT-SR).The detection-related abilities of these methods range from the detection of limited chromosome aneuploidy to comprehensive chromosome screening of the whole genome to differentiation of embryos with normal or balanced translocation/inversion karyotypes.In this study,we reviewed PGT-SR-related detection techniques to provide a better reference for clinical application and research.We have also discussed the potential development of novel techniques in the future.

Outcome of Couples with Reciprocal Translocation Carrier Undergoing the First Preimplantation Genetic Testing Cycles

Background: Reciprocal translocation(RCP) causes male infertility and female recurrent pregnancy loss. Male and female carriers have different responses to meiotic disturbances. Gender difference in outcomes of the RCP couples undergoing preimplantation genetic testing(PGT) is unknown.Methods: We conducted a retrospective analysis of 238 RCP couples(124 female and 114 male carriers) divided by gender of carrier from March 2014 to March 2017. Blastocysts were divided by day 5 and day 6. Females were divided into older(≥38 years) and younger(<38 years). Logistic regression was fitted for the relationship between gender of carriers and euploidy. Euploidy rate of each group, pregnancy rate, and live birth rate between different genders were analyzed.Results: The sperm live rate, forward motile sperm rate, and normal morphology rate of serum in male RCP group were significantly decreased. The euploidy rate was 30.30% in female group and 34.90% in male group(P = 0.131); 34.50% in day 5 group and 27.50% in day 6 group(P = 0.039); 33.40% in age <38 years group and 22.40% in age ≥38 years group(P = 0.063). Day 5(odds ratio [OR] = 1.388, 95% confidence interval [CI ] = 1.012–1.904; P = 0.042) and younger age(OR = 1.753, 95% CI = 0.97–3.17; P = 0.063) were associated with euploidy. The clinical pregnancy rate(37.90% vs. 41.20%), ongoing pregnancy rate(33.10% vs. 37.70%), and live birth rate(25.80% vs. 31.60%) per initiated were not significantly different in two gender groups.Conclusions: Although gender influence is not significant, couples with male carrier showed better clinical outcomes. The embryo growing rate and female age are important predictions estimating euploidy in RCP couples.

In vitro Fertilization with Single-nucleotide Polymorphism Microarray-based Preimplantation Genetic Testing for Aneuploidy Significantly Improves Clinical Outcomes in Infertile Women with Recurrent Pregnancy Loss:A Randomized Controlled Trial

Objective:To evaluate the effect of preimplantation genetic testing for aneuploidy(PGT-A)in infertile patients with recurrent pregnancy loss(RPL).Methods:A prospective randomized clinical trial was performed in a university-affiliated fertility center in Shanghai,China.Patients in the PGT-A group underwent blastocyst biopsy followed by single-nucleotide polymorphism microarray-based PGT-A and single euploid blastocyst transfer,whereas patients in the control group underwent routine in vitro fertilization/ICSI procedures and frozen embryo transfer of 1-2 embryos selected according to morphological standards.Results:Two hundred and seven infertile patients with RPL were included in this study and randomly assigned to either the control or the PGT-A group.Baseline variables and cycle characteristics were comparable between the two groups.The results showed that PGT-A significantly improved the ongoing pregnancy rate(55.34%vs.29.81%)as well as the live birth rate(48.54%vs.27.88%)and significantly reduced the miscarriage rate(0.00%vs.14.42%)on a per-patient analysis.A significant increase in cumulative ongoing pregnancy rates over time was observed in the PGT-A group.Subgroup analysis showed that the significant benefit diminished for patients who attempted≥2 PGT-A cycles.Conclusions:PGT-A significantly improved the ongoing pregnancy and live birth rate,while reduced miscarriage rate in infertile RPL patients.However,the significance diminished in patients attempting≥2 cycles;thus,further studies are warranted to explore the most cost-effective number of attempts in these patients to avoid overuse.

Genetic evaluation and testing for hereditary forms of cancer in the era of next-generation sequencing

The introduction of next-generation sequencing(NGS) technology in testing for hereditary cancer susceptibility allows testing of multiple cancer susceptibility genes simultaneously. While there are many potential benefits to utilizing this technology in the hereditary cancer clinic, including efficiency of time and cost, there are also important limitations that must be considered. The best panel for the given clinical situation should be selected to minimize the number of variants of unknown significance. The inclusion in panels of low penetrance or newly identified genes without specific actionability can be problematic for interpretation.Genetic counselors are an essential part of the hereditary cancer risk assessment team, helping the medical team select the most appropriate test and interpret the often complex results. Genetic counselors obtain an extended family history, counsel patients on the available tests and the potential implications of results for themselves and their family members(pre-test counseling), explain to patients the implications of the test results(post-test counseling), and assist in testing family members at risk.

Genetic Test of New Cottonwood Clonesat Nursery Stage

Twenty-five new clones belong to Populus Aigeiros of both domestic and foreign origin hadbeen introduced and tested at nursery stage in Shandong province. Results showed that height (H),diameter at stem base (D0) and survival rate (SR) varied significantly and genetic variation were very largeamong the clones. CVg and broad-sense heritability (h2) of H, D0 and SR of 1-year-old stock nursery were7.43%, 9.25%, 18.78% and 78.91%, 96.31%, 95.93%, respectively, showing high genetic control on thetested traits. 11 superior clones with characteristics of high growth rate and medium or high SR wereprimarily selected and genetic gains (△G) of H, D0 and SR were 16.89%, 16.08% and 13.08%, respectively.Rooting habits test of some selected clones were also conducted based on the cutting culture in watercontainer and annual growth increment measured. The date of first root emergence, number of main roots,number of lateral roots, length of main roots and the emergence date of growth peak varied to certain degreeamong the selected clones.

Character of cell-free genomic DNA in embryo culture medium and the prospect of its clinical application in preimplantation genetic testing

There is increasing evidence that cell-free DNA (cfDNA) in spent culture media (SCM) can be amplified for genetic testing. Therefore, this paper reviews the characteristics of cfDNA, including its fragment size, amount, origin, as well as some factors affecting the success rate of its amplification, together to provide researchers with a more comprehensive perspective on embryonic cfDNA. The origin of cfDNA in SCM is complicated and poses challenges to the interpretation of genetic test results. Advanced molecular techniques should distinguish between embryonic and contaminated DNA to maximize the success rate of amplification and analysis. Recent data showed that the type of culture medium, assisted hatching or not, the type of amplification kit, and fresh or thawed embryos were not related to the success rate of amplification, but the length of culture time might affect the success rate. The longer culture time, the more cfDNA is available in the SCM. Then we focused on the concordance between trophectoderm (TE), inner cell mass, whole embryo, and embryonic cfDNA. Despite successful amplification, the concordance between TE and embryonic cfDNA was low. In summary, non-invasive genetic testing using SCM could represent a major advance in future single embryo selection, however, contamination and timing for media collection are key factors affecting the results, and current non-invasive cfDNA testing should not be directly applied to clinical practice. Further research is needed to improve the methods used for testing techniques and genetic analysis to achieve greater accuracy and trace its origins before it can be used in the clinics.