Classification and genetic counselling for a novel splicing mutation of the MLH1 intron associated with Lynch syndrome in colorectal cancer

Background:Lynch-syndrome-associated cancer is caused by germline pathogenic mutations in mismatch repair genes.The major challenge to Lynch-syndrome screening is the interpretation of variants found by diagnostic testing.This study aimed to classify the MLH1 c.1989t5G>A mutation,which was previously reported as a variant of uncertain significance,to describe its clinical phenotypes and characteristics,to enable detailed genetic counselling.Methods:We reviewed the database of patients with Lynch-syndrome gene detection in our hospital.A novel variant of MLH1 c.1989t5G>A identified by next-generation sequencing was further investigated in this study.Immunohistochemical staining was carried out to assess the expression of MLH1 and PMS2 protein in tumour tissue.In silico analysis by Alamut software was used to predict the MLH1 c.1989t5G>A variant function.Reverse transcription-polymerase chain reaction and sequencing of RNA fromwhole bloodwere used to analyse the functional significance of this mutation.Results:Among affected family members in the suspected Lynch-syndrome pedigree,the patient suffered from late-stage colorectal cancer but had a good prognosis.We found the MLH1 c.1989t5G>A variant,which led to aberrant splicing and loss of MLH1 and PMS2 protein in the nuclei of tumour cells.An aberrant transcript was detectable and skipping of MLH1 exon 17 in carriers of MLH1 c.1989t5G>A was confirmed.Conclusions:MLH1 c.1989t5G>A was detected in a cancer family pedigree and identified as a pathological variant in patients with Lynch syndrome.Themutation spectrumof Lynch syndrome was enriched through enhanced genetic testing and close surveillancemight help future patients who are suspected of having Lynch syndrome to obtain a definitive early diagnosis.

Classification of osteogenesis imperfecta:Importance for prophylaxis and genetic counseling

Osteogenesis imperfecta(OI)is a genetically heterogeneous monogenic disease characterized by decreased bone mass,bone fragility,and recurrent fractures.The phenotypic spectrum varies considerably ranging from prenatal fractures with lethal outcomes to mild forms with few fractures and normal stature.The basic mechanism is a collagen-related defect,not only in synthesis but also in folding,processing,bone mineralization,or osteoblast function.In recent years,great progress has been made in identifying new genes and molecular mechanisms underlying OI.In this context,the classification of OI has been revised several times and different types are used.The Sillence classification,based on clinical and radiological characteristics,is currently used as a grading of clinical severity.Based on the metabolic pathway,the functional classification allows identifying regulatory elements and targeting specific therapeutic approaches.Genetic classification has the advantage of identifying the inheritance pattern,an essential element for genetic counseling and prophylaxis.Although genotype-phenotype correlations may sometimes be challenging,genetic diagnosis allows a personalized management strategy,accurate family planning,and pregnancy management decisions including options for mode of delivery,or early antenatal OI treatment.Future research on molecular pathways and pathogenic variants involved could lead to the development of genotype-based therapeutic approaches.This narrative review summarizes our current understanding of genes,molecular mechanisms involved in OI,classifications,and their utility in prophylaxis.

Two missense STK11 gene variations impaired LKB1/adenosine monophosphate-activated protein kinase signaling in Peutz-Jeghers syndrome

BACKGROUND Peutz-Jeghers syndrome(PJS)is a rare hereditary neoplastic disorder mainly associated with serine/threonine kinase 11(STK11/LKB1)gene mutations.Preimplantation genetic testing can protect a patient’s offspring from mutated genes;however,some variations in this gene have been interpreted as variants of uncertain significance(VUS),which complicate reproductive decision-making in genetic counseling.AIM To identify the pathogenicity of two missense variants and provide clinical guidance.METHODS Whole exome gene sequencing and Sanger sequencing were performed on the peripheral blood of patients with PJS treated at the Reproductive and Genetic Hospital of Citic-Xiangya.Software was employed to predict the protein structure,conservation,and pathogenicity of the two missense variation sites in patients with PJS.Additionally,plasmids were constructed and transfected into HeLa cells to observe cell growth.The differences in signal pathway expression between the variant group and the wild-type group were compared using western blot and immunohistochemistry.Statistical analysis was performed using one-way analysis of variance.P<0.05 was considered statistically significant.RESULTS We identified two missense STK11 gene VUS[c.889A>G(p.Arg297Gly)and c.733C>T(p.Leu245Phe)]in 9 unrelated PJS families who were seeking reproductive assistance.The two missense VUS were located in the catalytic domain of serine/threonine kinase,which is a key structure of the liver kinase B1(LKB1)protein.In vitro experiments showed that the phosphorylation levels of adenosine monophosphate-activated protein kinase(AMPK)at Thr172 and LKB1 at Ser428 were significantly higher in transfected variation-type cells than in wild-type cells.In addition,the two missense STK11 variants promoted the proliferation of HeLa cells.Subsequent immunohistochemical analysis showed that phosphorylated-AMPK(Thr172)expression was significantly lower in gastric,colonic,and uterine polyps from PJS patients with missense variations than in non-PJS patients.Our findings indicate that these two missense STK11 variants are likely pathogenic and inactivate the STK11 gene,causing it to lose its function of regulating downstream phosphorylated-AMPK(Thr172),which may lead to the development of PJS.The identification of the pathogenic mutations in these two clinically characterized PJS patients has been helpful in guiding them toward the most appropriate mode of pregnancy assistance.CONCLUSION These two missense variants can be interpreted as likely pathogenic variants that mediated the onset of PJS in the two patients.These findings not only offer insights for clinical decision-making,but also serve as a foundation for further research and reanalysis of missense VUS in rare diseases.

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.

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.

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.

Genetic counseling in post-genomic era: Don't pretend to know the meaning of a gene mutation if you don't know

In this post-genomic era, more and more susceptibility loci of many possible genetic diseases are published. As our knowledge about these susceptibility loci is limited and partial, we should be very careful and responsible when patients seek genetic counseling about these possible genetic diseases. We should apply Confucius' s principle about knowledge and information to genetic conseling, and tell the truth to our patients about what we know and what we do not know. Like many other cancers, breast cancer is a very complicated, multifactorial disease; genetic factors, lifestyles and eating habits, environmental factors, and viral infections might be involved in breast cancer; hence, it is difficult to figure out the real etiology of breast cancer. It is not crystal clear that a person who carries mutations of the breast cancer 1, early onset and/or breast cancer 2, early onset genes would eventually get breast cancer in her/his lifetime. No person should undergo a preventive double mastectomy, unless we know the etiology of breast cancer someday.

Profile of Patients Attended at the Genetic Service of a Special Care Institution in Brazil

Objective： To analyze the main etiological diagnoses of patients attended at a genetics outpatient clinic of the Association of Parents and Friends of Exceptional Children/APAE in the state of Amazonas, Brazil. Methods： retrospective study of patients seen in the period 2005-2016, with review of medical records. The following data were recorded： sex, origin of referral and etiological diagnosis. Results： 362 patients were attended, 94.7% of them from Manaus, and 5.3% from the interior of the state. The etiological diagnosis was defined in 262 （72.3%） of the sample, of which 254 （70.2%） were of genetic etiology and 8 （2.2%） non-genetic. Of the genetic etiologies, 46 （12.7%） cases were monogenic syndromes, 136 （37.6%） were chromosomal aberrations and 72 （19.9%） had multifactorial causes, however, 100 （27.6%） cases remained unclear. There were several syndromes found, with Down syndrome being the most frequent and correlating significantly with the sex of the patient （male predominance, p 〈 0.05）. Conclusions： The study carried out in the APAE/Manaus genetics outpatient clinic allowed the profile of the patients being attended to be traced. It was verified that the majority of the patients were male and that the diagnosis of chromosomal alterations was the most frequent.

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.

Hereditary pancreatitis

Hereditary pancreatitis is an autosomal dominant condition,which results in recurrent attacks of acute pancreatitis,progressing to chronic pancreatitis often at a young age.The majority of patients with hereditary pancreatitis expressone of two mutations (R122H or N29I) in the cationictrypsinogen gene (PRSS1 gene). It has been hypothesisedthat one of these mutations, the R122H mutation causespancreatitis by altering a trypsin recognition site sopreventing deactivation of trypsin within the pancreas andprolonging its action, resulting in autodigestion. Families withthese two mutations have been identified in many countriesand there are also other rarer mutations, which have alsobeen linked to hereditary pancreatitis.Patients with hereditary pancreatitis present in the sameway as those with sporadic pancreatitis but at an earlierage. It is common for patients to remain undiagnosed formany years, particularly ifthey present with non-specificsymptoms. Hereditary pancreatitis should always beconsidered in patients who present with recurrent pancreatitiswith a family history of pancreatic disease. If patients withthe 2 common mutations are compared, those with theR122H mutation are more likely to present at a younger ageand are more likely to require surgical intervention than thosewith N29I. Hereditary pancreatitis carries a 40 % lifetimerisk of pancreatic cancer with those patients aged between50 to 70 being most at risk in whom screening tests maybecome important.

Six families with balanced chromosome translocation associated with reproductive risks in Hainan Province: Case reports and review of the literature

BACKGROUND Balanced translocation refers to the process where breakage and reconnection of chromosomes occur at abnormal positions.As the genetic substance with balanced translocation in individuals does not change,which is usually characterized by normal phenotype and intelligence,the individuals seek medical service after many miscarriages,resulting in considerable mental and physical burdens of the family members.In the current era with rapid advances in detection technology,cytogenetic examination,as a definitive approach,still plays an essential role.CASE SUMMARY We report six cases with balanced chromosome translocation:Case 1:46,XY,t(3;12)(q27;q24.1),infertility after 3 years of marriage;Case 2:46,XX,t(4;16)(q31;q12),small uterus and irregular menstruation;Case 3:46,XY,t(4;5)(q33;q13),9qh+,not pregnant after arrested fetal development;Case 4:46,XX,t(11;17)(q13;p11.2),not pregnant after two times of spontaneous abortion;Case 5:46,XX,t(10;13)(q24;q21.2),not pregnant after arrested fetal development for once;Case 6:46,XX,t(1;4)(p36.1;q31.1),not pregnant after arrested fetal development for two times.The first four cases had chromosomal aberration karyotypes.CONCLUSION These results suggested that balanced chromosomal translocation carriers are associated with reproductive risks and a very high probability of abnormal pregnancy.The discovery of the first four reported chromosomal aberration karyotypes provides an important basis for studying the occurrence of genetic diseases.

Prenatal diagnosis of spinocerebellar ataxia type 3/Machado-Joseph disease in China's Mainland A case report

Spinocerebellar ataxia type 3/Machado-Joseph disease （SCA3/MJD） is a progressive, currently untreatable and ultimately fatal ataxic disorder that belongs to the group of neurological disorders known as CAG-repeat or polyglutamine diseases. Here, we present the first prenatal diagnosis of SCA3/MJD in China's Mainland in a woman who was known to carry an expanded CAG-trinucleotide repeat in the MJD1 gene. After evaluating motivation and psychological tolerance of the couple, amniocentesis was performed after 14 weeks of gestation. Polymerase chain reactions followed by T-vector cloning and direct sequencing were employed to evaluate the CAG-repeat number of the fetal MJD1 gene. We identified a truncated CAG expansion of 78 repeats in the MJD1 gene of the fetus compared with 81 repeats in his mother.

Germline mutations in hereditary diffuse gastric cancer

Gastric cancer is one of the leading causes of cancer-related deaths worldwide. Among which, about 1%–3% of gastric cancer patients were characterized by inherited gastric cancer predisposition syndromes, knowing as hereditary diffuse gastric cancer（HDGC）. Studies reported that CDH1 germline mutations are the main cause of HDGC. With the help of rapid development of genetic testing technologies and data analysis tools, more and more researchers focus on seeking candidate susceptibility genes for hereditary cancer syndromes. In addition, National Comprehensive Cancer Network（NCCN） guidelines recommend that the patients of HDGC carrying CDH1 mutations should undergo prophylactic gastrectomy or routine endoscopic surveillances. Therefore, genetic counseling plays a key role in helping individuals with pathogenic mutations make appropriate risk management plans. Moreover, experienced and professional genetic counselors as well as a systematic multidisciplinary team（MDT） are also required to facilitate the development of genetic counseling and benefit pathogenic mutation carriers who are in need of regular and standardized risk management solutions. In this review, we provided an overview about the germline mutations of several genes identified in HDGC, suggesting that these genes may potentially act as susceptibility genes for this malignant cancer syndrome. Furthermore, we introduced information for prevention, diagnosis and risk management of HDGC. Investigations on key factors that may have effect on risk management decision-making and genetic data collection of more cancer syndrome family pedigrees are required for the development of HDGC therapeutic strategies.

Renal Tubular Dysgenesis Associated with Compound Heterozygous ACE Mutations

Inherited renal tubular dysgenesis(RTD),a rare,autosomal recessive disorder is caused by mutations in the genes encoding components of the renin-angiotensin pathway:angiotensinogen(AGT),renin(REN),angiotensin-converting enzyme(ACE),and angiotensinΙΙreceptor type 1(AGTR1).It characterized by the absence or poor development of renal tubules,and associated with oligohydramnios,Potter sequence and neonatal death due to renal or respiratory failure.We report a family with two mutations in the coding region of the ACE gene:a nonsense mutation in exon4(c.538C>T)and a frameshift deletion at nucleotide 3073 and nucleotide 3074 in exon20(c.3073_3074delTC).The mutations were in the compound heterozygous state causing disease,because each parent had their own mutation.

Genetic counseling, prenatal screening and diagnosis of Down syndrome in the second trimester in women of advanced maternal age： a prospective study

Background The incidence of autosomal trisomy in livebirths is strongly dependent on maternal age. Special consideration is given to the provision of prenatal screening and cytogenetic testing to women of advanced maternal age （AMA）. The aim of this study was to evaluate the effectiveness of second trimester prenatal screening and amniocentesis for Down syndrome （DS） and compare the trends of choice of screening and amniocentesis among AMA women. Methods A total of 5404 AMA patients with natural singleton pregnancy were recruited for this prospective study from January 2008 to December 2010. The gestational weeks were from 15 weeks to 20~6 weeks. The patients referred were grouped into a screening group （2107 cases） and an amniocentesis group （3297 cases） by their own decision. The prevalence of DS was compared between the two groups by chi-square test. Choice rates for each maternal age with trends were compared by regression analysis. Results There were 18 cases of fetal DS detected in the screening group with a prevalence of 8.54%o （18/2107）. Twenty- five cases of fetal DS were diagnosed in the amniocentesis group with a prevalence of 7,58%0 （25/3297）. No statistical difference was observed in the prevalence of DS between the screening and amniocentesis group （P=0.928）. The invasive testing rate for DS in the amniocentesis group was 5.54 times higher than that of the screening group （1/131.88 vs. 1/23.78）. With the increase of the maternal age, the choice of amniocentesis increased while the choice of the screening showed an opposite trend. The choice of the AMA women between the screening and amniocentesis was significantly age relevant （P=0.012）. Conclusions The second trimester serum screening age alone to screen for DS. We suggest educating screening and amniocentesis options. in combination with maternal age was more effective than maternal the patients by recommending AMA women be informed of both

Evaluating chromosomal segregation in a family where both spouses carry an autosomal translocation

Autosomal reciprocal translocations represent exchanges of chromatin fragments between non-homologous chromosomes.Translocations are facilitated by the creation of quadrivalent structures during the first meiotic division,which are characterized by the length of the translocated and centric segments,asymmetry,and the presence of terminal breakpoints,all of which may impact segregation mode.Here,we report a rare case of multiple reciprocal translocations within a single family.This includes the evaluation of the translocations in each of the spouses and an analysis of their chromosome segregation patterns as determined by the constellation of universal characteristics in each of their quadrivalents.The obtained results will be of interest to fundamental biology,as they will expand the understanding of the factors affecting chromosome segregation during meiosis.

New Insights into Genotype-phenotype Correlations in Chinese Facioscapulohumeral Muscular Dystrophy： A Retrospective Analysis of 178 Patients

Background： Facioscapulohumeral muscular dystrophy （FSHD）, a common autosomal dominant muscular disorder, is caused by contraction of the D4Z4 repeats on 4q35. The complicated genotype-phenotype correlation among different ethnic population remains a controversial subject. We aimed to refine this correlation in order to provide new information for genetic counseling. Methods： Here, a cohort of[36 Chinese families including 178 affected individuals and 137 unaffected members were investigated. Genetic analyses were pertbrmed using the pl 3E-11, 4qA and 4qB probes after pulsed field gel electrophoresis separation and southern blotting. A I 0-grade FSHD clinical severity scale was adopted for clinical assessment. The genotype-phenotype correlation was established by linear regression analyses. Results： We observed a roughly inversed correlation between the short EcoRl fragment size and age-corrected clinical severity score in 154 symptomatic patients （P 〈 0.05）. Compared to male patients, a significant higher proportion of females in both asymptomatic carriers and severe patients showed larger variation in the size of short EcoRI fragment. A high incidence （ 19/42, 45.2%） ofasymptomatic （or minimally affected） carriers was found in familial members. Conclusions： Although the number of D4Z4 repeats is known as one of the critical influences on genotype-phenotype correlation, a rnajority ofphenotypic spectrum was still incompatible with their heterozygous contraction of the D4Z4 repeat, especial in female cases. Our resuhs suggest that there are multi-factors synergistically modulating the phenotypic expression.

Prenatal Testing or Screening?

Over the past 50 years,the scope and extent of prenatal diagnosis and screening for genetic disorders have improved geometrically.There has been a pendulum like swing from testing to screening back and forth as new technologies emerge.The concurrent developments of cell free fetal DNA analysis of maternal blood has dramatically changed patient’s choices towards screening.However,with the use of array comparative genomic hybridization of fetal DNA that requires diagnostic procedures(Chorionic villus sampling and amniocentesis),much more extensive diagnosis can be obtained.Until noninvasive methods can replicate what can be done with diagnostic procedures there still will be a"price to be paid"for opting for the non-invasive methods.