Clinical Genetic Counseling Research Articles

A Delphi study to prioritize genetic counseling outcomes: What matters most.

Research on genetic counseling outcomes has examined a range of metrics many that differ in quality and extent of psychometric assessment and in some cases fail to encompass potential benefits of genetic counseling for patients. Although a variety of possible outcomes have been explored, selecting the most important or relevant outcomes and identifying well-validated measures remain challenging. An online, modified Delphi method was used to prioritize genetic counseling outcomes from the viewpoint of individuals from four stakeholder groups - clinical genetic counselors, outcome researchers, genetic counseling training directors, and genetic counseling consumers/advocates. A survey of 181 genetic counseling outcomes were rated based on perceived importance and then sorted and categorized using the Framework for Outcomes of Clinical Communication Services in Genetic Counseling (FOCUS-GC) framework. Three of the FOCUS-GC domains (Process, Patient Care Experience, and Patient Changes) were assessed as most important, while none of the most highly rated outcomes fell into the domains of Patient Health or Family Changes. The majority of outcomes deemed most important by stakeholder groups were within the process domain. When looking at the proportion of outcomes that overlapped with the consumer group, clinical genetic counselors had the highest degree of similarity with consumers when looking at the high relative importance band outcomes (61.1% overlap), followed by training directors (58.3%), and outcome researchers (41.7%). Variability in importance according to stakeholder groups was an important consideration and prioritizing outcomes was challenging given that the majority of outcomes were rated as important. Working to bridge the realities of clinical care and fundamental differences in the viewpoints and priorities of genetic counseling research directions is an area for future exploration.

Identification of a novel c.1A>G variant of GDAP1 gene in a pedigree affected with autosomal recessive fibula atrophy

To explore the genetic basis for a pedigree affected with Charcot-Marie-Tooth (CMT) disease through high-throughput sequencing. Potential variants of the genes associated with CMT were screened by next-generation sequencing (NGS) of the members of the pedigree. NGS has revealed that the two affected sisters both harbored homozygous c.1A>G variant of the GDAP1 gene, which caused replacement of the first amino acid Methionine by Valine (p.Met1Val). Their parents were both carriers of the heterozygous c.1A>G variant. The variant was unreported previously and has an extremely low frequency in the population. Meanwhile, one of the sisters and the mother also carried heterozygous c.710A>T variant of the BAG3 gene. The homozygous c.1A>G variant of the GDAP1 gene probably underlay the CMT in both children. Above result has enabled clinical diagnosis and genetic counseling for this pedigree.

A Splicing Variant in OCRL Gene Might Explain the Second Case of Lowe Syndrome in Iran

: Lowe syndrome is a condition that primarily affects eyes, brain, and kidneys. This disorder follows X-linked recessive mode of inheritance and it occurs in males mainly. Mutations in OCRL (located at Xq25) gene can cause accumulation of phosphatidylinositol bisphosphate and disturbed actin cytoskeleton remodeling. There are 268 mutations in OCRL gene causing Lowe syndrome or Dent disease 2 in HGMD database, however 10 - 20% of Lowe syndrome suspects remain undiagnosed at molecular level. Here we present a male case of Lowe syndrome with characteristic features. Comprehensive clinical examination and genetic counseling were performed. Sanger sequencing was employed to investigate the possible OCRL mutations and we identified a donor splice site variant (NM-000276: c.2469 + 1G > A) in hemizygous state. This is a pathogenic variant according to the ACMG standards and guidelines and might explain the clinical features of the patient. This result is in accordance with the clinical diagnosis of Lowe syndrome and it is absent from ExAC, 1000 G, Iranome, GME, gnomAD Genome databases of healthy controls. In-silico analysis of this splicing variant revealed that the position is highly conserved between species. Splicing prediction tools predicted some changes in splicing pattern of the OCRL transcript, elimination of some protein features, and malfunctioning the OCRL protein as a consequence of this variant. Accordingly, we proposed the c.2469 + 1G > A variant might explain the clinical features in studied patient and be employed for prenatal diagnosis of Lowe syndrome in the family.

The Canadian genetic counseling workforce: Perspectives from employers and recent graduates.

There is a lack of literature devoted to the Canadian genetic counseling workforce. Current and prospective genetic counseling students, graduates, employers, programs, and funding agencies remain largely uninformed of trends in the job market. The purpose of this study was to investigate the employment experiences of recent Canadian genetic counseling graduates and employers of genetic counselors (GCs) in Canada. An online survey was distributed to Canadians who had graduated from North American genetic counseling programs from 2014 to 2018 and to employers with experience hiring patient-facing genetic counselors from 2016 to 2018. Quantitative data were analyzed through descriptive statistics and, where appropriate, logistic regression. Qualitative data were reviewed to illustrate and support the quantitative data. Half of the employer responders (11/22) reported hiring more or many more genetic counselors compared to 3years ago (2016), and a majority (n=19, 86%) reported a desire to hire at least one more genetic counselor if funding were available. Most graduates (45/70, 64%) reported securing employment before graduation, 33% (n=23) within 6months of graduation, and no one taking longer than 1year. For recent graduates, location was the most important factor when looking for work, and those who chose to work in Canada experienced significantly more challenges gaining employment as opposed to those who worked internationally (p=0.03). The specialties in highest demand for genetic counselors and the most common areas of practice for recent graduates included adult general genetics, prenatal genetics, and cancer genetics. Overall, our findings suggest that there is a growth of employment opportunities in Canada and more employer-reported need for clinical genetic counselors; however, there is a lack of funding to support this expansion.

Breast cancer polygenic risk scores in the clinical cancer genetic counseling setting: Current practices and impact on patient management.

Multivariate risk models are commonly used in clinical practice to estimate a woman's lifetime risk for breast cancer and assist in implementation of appropriate screening and risk reduction strategies. More recently, breast cancer polygenic risk scores (PRS) have been derived and integrated into these models to further improve risk estimation. While breast cancer PRS have been offered by two clinical diagnostic laboratories since 2017, little is known about the extent to which genetic counselors are ordering breast cancer PRS or incorporating the results into patient management. This study surveyed U.S. cancer genetic counselors from October 2019 to January 2020 to identify and understand their current practices with breast cancer PRS, to determine the impact of breast cancer PRS on patient management, and to anticipate future genetic counselor practices with breast cancer PRS. Fewer than half of respondents (43%, 51/120) had ordered breast cancer PRS and approximately one-third (35%, 16/46) reported that the PRS had changed their medical management recommendations. The majority of cancer genetic counselors had not ordered PRS, most commonly due to (a) lack of clinical guidelines (90%, 60/67), (b) insufficient evidence of clinical utility (88%, 59/67), and (c) lack of availability for patients of non-European ancestry (70%, 47/67). Of genetic counselors who had not ordered breast cancer PRS, only 10% (7/68) did not believe they would order PRS in the future. This is the first study to characterize genetic counselors' experiences with breast cancer PRS. Results from this study indicate that although breast cancer PRS have been clinically available for patients for several years, most cancer genetic counselors are not yet convinced they are ready to be incorporated into patient care.

Please Wait for the Host to Start This Meeting: A Push for H.R. 3235 Amid COVID-19.

Please Wait for the Host to Start This Meeting: A Push for H.R. 3235 Amid COVID-19.

IMPLICATIONS IN DIAGNOSING CYSTIC FIBROSIS IN AN ELDERLY WOMAN

SESSION TITLE: Medical Student/Resident Genetic and Developmental Disorders Posters SESSION TYPE: Med Student/Res Case Rep Postr PRESENTED ON: October 18-21, 2020 INTRODUCTION: Cystic fibrosis (CF) is the most common lethal genetic disease for Caucasians and is typically a diagnosis of young children, and is rare to be diagnosed in adults, let alone new diagnosis in those greater than 80 years of age. The majority of new diagnoses are made on newborn screening tests, however cystic fibrosis should still be considered in adults who have a family history, hemoptysis, chronic pansinusitis, productive cough, and bronchiectasis. CASE PRESENTATION: DS is an 85 year old female with history of esophageal achalasia, but no prior history of recurrent infections, sinus disease or pulmonary symptoms who presented to pulmonary clinic for evaluation of several months of a non-productive cough. A CT scan showed right middle lobe bronchiectasis with surrounding tree in bud infiltrates. She completed treatment for presumed bronchitis with ciprofloxacin and azithromycin without a change in her symptoms. A repeat chest xray showed progression of right middle lung infiltrates. She had no high risk epidemiologic factors for tuberculosis, so the initial concern was for nontuberculous mycoplasma or silent aspiration pneumonitis given esophageal achalasia. She had a bronchoscopy showing copious secretions and a bronchoalveolar lavage culture grew burkholderia gladioli. She completed 2 weeks of levofloxacin with initial improvement, but shortly after noticed recurrence of symptoms. She had been using incentive spirometry, percussive therapy and bronchodilators without significant changes, however was able to hike in Colorado and relatively asymptomatic from pulmonary perspective aside from a chronic cough. A sweat chloride test was notable for a value > 60mmol/L concerning for a diagnosis of cystic fibrosis. Genetic studies were positive for 2 CFTR gene mutations, pathogenic variant c.3144T>G and variant of unknown significance c.125C>T. She was informed and discussed the following with her 3 children and relatives. At this time, she has elected to avoid future treatment given minimal symptoms. DISCUSSION: Although our patient did not pursue treatment, the diagnosis of CF has important implications for her family. CF is inherited in an autosomal recessive pattern, so knowledge of family members carrying the trait becomes a factor in regards to family planning. Those with CF have described shorter life spans, personal health, and potential impact of CF on a child as factors to consider during family planning. Genetic testing assists with family planning, as each CFTR genetic mutation can present differently, and is an important factor when considering emerging therapies that target defective CFTR proteins with promising results. CONCLUSIONS: In conclusion, despite CF being primarily a diagnosis discovered in infancy or early childhood, the importance of keeping CF in the differential in older adults presenting with bronchiectasis has consequences for their families and future children. Reference #1: Osullivan, B. P., & Freedman, S. D. (2009). Cystic fibrosis. The Lancet, 373(9678), 1891–1904. doi: 10.1016/s0140-6736(09)60327-5 Reference #2: Moskowitz, S. M., Chmiel, J. F., Sternen, D. L., Cheng, E., Gibson, R. L., Marshall, S. G., & Cutting, G. R. (2008). Clinical practice and genetic counseling for cystic fibrosis and CFTR-related disorders. Genetics in medicine: official journal of the American College of Medical Genetics, 10(12), 851–868. https://doi.org/10.1097/GIM.0b013e31818e55a2 Reference #3: Traxler, S. A., Chavez, V., Hadjiliadis, D., Shea, J. A., Mollen, C., & Schreiber, C. A. (2019). Fertility considerations and attitudes about family planning among women with cystic fibrosis. Contraception, 100(3), 228–233. doi: 10.1016/j.contraception.2019.05.005 DISCLOSURES: No relevant relationships by Katie Adib, source=Web Response No relevant relationships by Vincent Esguerra, source=Web Response No relevant relationships by Stephen Kirkby, source=Web Response No relevant relationships by Nihal Patel, source=Web Response

Germline variants of Brazilian women with breast cancer and detection of a novel pathogenic ATM deletion in early-onset breast cancer.

It is estimated that 5-10% of breast cancer cases are hereditary. The identification of pathogenic germline variants allows individualized preventive health care, improvement of clinical management and genetic counseling. Studies in ethnically admixed Latin American populations have identified regions with increased frequency of deleterious variants in breast cancer predisposing genes. In this context, the Brazilian population exhibits great genetic heterogeneity, and is not well represented in international databases, which makes it difficult to interpret the clinical relevance of germline variants. We evaluated the frequency of pathogenic/likely pathogenic (P/LP) germline variants in up to 37 breast cancer predisposing genes, in a cohort of 105 breast and/or ovarian cancer Brazilian women referred to two research centers between 2014 and2019. A total of 22 patients (21%) were found to carry P/LP variants, and 16 VUS were detected in 15 patients (14.3%). Additionally, a novel pathogenic ATM intragenic deletion was identified in an early-onset breast cancer. We also detected a BRCA1 pathogenic variant (c.5074+2T>C) in higher frequency (10×) than in other studies with similar cohorts. Our findings contribute to the characterization of the genetic background of breast cancer predisposition in the Brazilian population as a useful resource to discriminate between deleterious variants and VUS, thus enabling improvement in the preventive health care and clinical management of carriers.

First report of the spectrum of δ-globin gene mutations among women of reproductive age in Fujian area-Discrimination of δ-thalassemia, α-thalassemia, and Iron Deficiency Anemia.

BackgroundLow HbA2 level is an underlying of δ‐thalassemia, α‐thalassemia, and IDA. Interactions of these disorders can generate a wide spectrum of phenotype, which will pose diagnostic conundrum for clinical assessment, carrier screening, and genetic counseling.MethodsSubjects with HbA2 levels below 2.0% with normal or reduced hematological parameters were recruited for further investigation. δ‐globin gene mutations were identified by DNA sequencing of the HBD gene. Serum ferritin (SF) concentration was determined by the chemiluminescent microparticle immunoassay. The three common deletional α‐thalassemia (‐‐SEA/αα, ‐α3.7/αα, and ‐α4.2/αα) were detected using Gap‐PCR, detection of the point mutations in the three nondeletional α‐thalassemia (αCSα/αα,αQSα/αα,αWSα/αα), and the 17 common β‐thalassemia was performed using reverse dot blot hybridization (RDB).ResultsWe had characterized the δ‐globin gene mutations in 20 cases, revealing a frequency of 0.4% in the women of reproductive age (20/4 792). Two previously known mutations:‐77 T > C and −30 T > C and 3 novel δ‐globin gene defects: −44G > A,CD87C > T, and CD134T > A were found. In the selected cases, we also found 85 cases confirmed with (51.2%,85/166) IDA and 39 cases (23.5%,39/166) with common α‐thalassemia. Subjects with δ‐thalassemia had statistically higher levels of Hb, MCV, and MCH compared with other two groups, whereas statistically lower levels of RDW were seen in δ‐thalassemia group. What's more, statistically higher levels of SF were seen in δ‐thalassemia group, compared with IDA groups.ConclusionWe reported the spectrum of δ‐thalassemia mutations for the first time with the frequency of 0.4% among women of reproductive age in Fujian area and found that −77T > C mutation was the most common mutation, followed by −30T > C mutation. What's more, 3 novel δ‐globin gene defects: −44G > A,CD87C > T and CD134T > A were found. A thorough analysis of the hematological, electrophoretic characterization, and the level of SF was needed to suspect and further investigate the existence of IDA, α‐thalassemia, and δ‐thalassemia.

Need for a precise molecular diagnosis in Beckwith-Wiedemann and Silver-Russell syndrome: what has to be considered and why it is important

Molecular diagnostic testing of the 11p15.5-associated imprinting disorders Silver-Russell and Beckwith-Wiedemann syndrome (SRS, BWS) is challenging due to the broad spectrum of molecular defects and their mosaic occurrence. Additionally, the decision on the molecular testing algorithm is hindered by their clinical heterogeneity. However, the precise identification of the type of defect is often a prerequisite for the clinical management and genetic counselling. Four major molecular alterations (epimutations, uniparental disomies, copy number variants, single nucleotide variants) have been identified, but their frequencies vary between SRS and BWS. Due to their molecular aetiology, epimutations in both disorders as well as upd(11)pat in BWS are particular prone to mosaicism which might additionally complicate the interpretation of testing results. We report on our experience of molecular analysis in a total cohort of 1448 patients referred for diagnostic testing of BWS and SRS, comprising a dataset from 737 new patients and from 711 cases from a recent study. Though the majority of positively tested patients showed the expected molecular results, we identified a considerable number of clinically unexpected molecular alterations as well as not yet reported changes and discrepant mosaic distributions. Additionally, the rate of multilocus imprinting disturbances among the patients with epimutations and uniparental diploidies could be further specified. Altogether, these cases show that comprehensive testing strategies have to be applied in diagnostic testing of SRS and BWS. The precise molecular diagnosis is required as the basis for a targeted management (e.g. ECG (electrocardiogram) and tumour surveillance in BWS, growth treatment in SRS). The molecular diagnosis furthermore provides the basis for genetic counselling. However, it has to be considered that recurrence risk calculation is determined by the phenotypic consequences of each molecular alteration and mechanism by which the alteration arose.Key messagesThe detection rates for the typical molecular defects of Beckwith-Wiedemann syndrome or Silver-Russell syndrome (BWS, SRS) are lower in routine cohorts than in clinically well-characterised ones.A broad spectrum of (unexpected) molecular alterations in both disorders can be identified.Multilocus imprinting disturbances (MLID) are less frequent in SRS than expected.The frequency of MLID and uniparental diploidy in BWS is confirmed.Mosaicism is a diagnostic challenge in BWS and SRS.The precise determination of the molecular defects affecting is the basis for a targeted clinical management and genetic counselling.

Pedigree Analysis of Nonhomologous Sequence Recombination of HBA1 and HBA2 Genes

The aim of this study was to investigate a family with nonhomologous sequence recombination of HBA1 and HBA2 genes and provide a favorable basis for genetic counseling and eugenics. Peripheral blood of family members was collected. Hematological parameters were determined by an automated cell counter and hemoglobin (Hb) analysis was performed using high performance liquid chromatography (HPLC). Villus samples were taken for prenatal diagnosis (PND). Gap-polymerase chain reaction (gap-PCR) and reverse dot-blot were used for thalassemia genotyping. DNA sequencing was used to analyze the gene sequence of HBA1 (α1-globin) and HBA2 (α2-globin). The nonhomologous sequence recombination allelic variant of HBA1 and HBA2 genes were identified, namely, a gene conversion on the HBA2 gene called α12 (HBA12). The α12 allele consists primarily of the HBA2 gene sequence except for a segment of the IVS-II in which HBA2-specific sequences have been replaced by HBA1-specific sequences. The following genotypes were observed: – –SEA/αα12 (Southeast Asian deletion), αα/αα12 and αQSα/αα12 (Hb Quong Sze or Hb QS; HBA2: c.377T>C), and all manifested as small cell hypochromic anemia. To find the α12 allele in the Chinese population and clarify the influence of the α12 allele and its common inheritance with abnormal Hb and α-thalassemia (α-thal) on α-globin gene expression can help guide clinical diagnosis and genetic counseling.

Digenic inheritance of MSH6 and MUTYH variants in familial colorectal cancer.

We describe a family severely affected by colorectal cancer (CRC) where whole‐exome sequencing identified the coinheritance of the germline variants encoding MSH6 p.Thr1100Met and MUTYH p.Tyr179Cys in, at least, three CRC patients diagnosed before 60 years of age. Digenic inheritance of monoallelic MSH6 variants of uncertain significance and MUTYH variants has been suggested to predispose to Lynch syndrome‐associated cancers; however, cosegregation with disease in the familial setting has not yet been established. The identification of individuals carrying multiple potential cancer risk variants is expected to rise with the increased application of whole‐genome sequencing and large multigene panel testing in clinical genetic counseling of familial cancer patients. Here we demonstrate the coinheritance of monoallelic variants in MSH6 and MUTYH consistent with cosegregation with CRC, further supporting a role for digenic inheritance in cancer predisposition.

Genetic study of a child with developmental delay and mental retardation

To explore the genetic basis for a child with developmental delay and mental retardation. Chromosomal karyotype of the child was analyzed by G-, C- and N-banding techniques. Her genome DNA was analyzed with single nucleotide polymorphisms array (SNP array). The result was validated by fluorescence quantitative polymerase chain reaction (PCR). The karyotype of the child was ascertained as 46,XX,r(22)(p12q13). SNP array has revealed a deletion of approximately 1.4 Mb at 22q13.33 (49 802 963-51 197 766). The deletion has encompassed the SHANK3, a crucial gene for the development of nervous system. Fluorescence quantitative PCR has confirmed the deletion of exons 7, 19 and 22 of the SHANK3 gene. The phenotype of the patient may be attributed to the microdeletion at 22q13.33. Cytogenetic methods combined with SNP array and fluorescence quantitative PCR can identify aberrant chromosomes and provide accurate information for the clinical diagnosis and genetic counseling.

Clinical genetic testing and counselling in autism spectrum disorder

Abstract Autism spectrum disorders (ASDs) are phenotypically as well as genetically heterogeneous developmental disorders with a strong heritability. Clinical and basic science research has described many replicated genetic risk factors. Many findings can well be translated into clinical human genetic practice. The current article summarizes results of genetic studies in ASD, provides a diagnostic algorithm for the clinical human genetic work-up reflecting the German health care system options and gives information with regard to the obligatory genetic counselling after a clinical genetic assessment.

Clinical and laboratory interpretation of mitochondrial mRNA variants

Interpretation of mitochondrial protein-encoding (mt-mRNA) variants has been challenging due to mitochondrial characteristics that have not been addressed by American College of Medical Genetics and Genomics guidelines. We developed criteria for the interpretation of mt-mRNA variants via literature review of reported variants, tested and refined these criteria by using our new cases, followed by interpreting 421 novel variants in our clinical database using these verified criteria. A total of 32 of 56 previously reported pathogenic (P) variants had convincing evidence for pathogenicity. These variants are either null variants, well-known disease-causing variants, or have robust functional data or strong phenotypic correlation with heteroplasmy levels. Based on our criteria, 65.7% (730/1,111) of variants of unknown significance (VUS) were reclassified as benign (B) or likely benign (LB), and one variant was scored as likely pathogenic (LP). Furthermore, using our criteria we classified 2, 12, and 23 as P, LP, and LB, respectively, among 421 novel variants. The remaining stayed as VUS (91.2%). Appropriate interpretation of mt-mRNA variants is the basis for clinical diagnosis and genetic counseling. Mutation type, heteroplasmy levels in different tissues of the probands and matrilineal relatives, in silico predictions, population data, as well as functional studies are key points for pathogenicity assessments.

Utilization of clinical genetic counseling among childhood and young adult cancer survivors in a registry trial.

We describe utilization of clinical genetic services among survivors of childhood and young adult cancer after participation in a genetic registry. Clinical genetic counselors flagged 162 out of 1069 pedigrees (15.2%) as suggestive of inheritable cancer susceptibility, resulting in 126 (11.8%) referral letters. Following delivery of the referral letters, 19 (15.1%) participants completed clinical genetic counseling, 16 (12.7%) received testing, and four (3.2%) were found to have actionable results. Our results suggest a discordance between reported willingness to undergo genetic counseling and real-world utilization.

Serum 25 hydroxyvitamin D levels and affecting factors among preconception fertile women

BackgroundRecent study found that vitamin D before conception was considered as a potential additional determinant for achieving pregnancy and live births. The study aimed to evaluate the serum 25 hydroxyvitamin D (25(OH)D) levels and its affecting factors among preconception fertile women.MethodsThis cross-sectional study enrolled 410 women aged 22–44 years who attended a preconception genetic counseling clinic from January 2018 to May 2019. Sociodemographic characteristics and reproductive history of women were collected, and height and weight were measured. Serum 25(OH)D concentration was assayed with chemiluminescence immunoassay. Descriptive statistics were used to examine serum 25(OH)D concentration, and socio-demographic characteristics and reproductive history among preconception women. Determinants of vitamin D deficiency and its affecting factors were assessed using χ2 test and logistic regression.ResultsFindings showed 84.4% of women had serum 25(OH)D concentration below 20 ng/mL. Women working indoors as well as without a history of childbirth had significantly lower 25(OH)D levels compared with those non-working individuals and having delivered a previous child (both P < 0.05). The 25(OH)D levels were the lowest in winter among that in spring, summer, and autumn (all P < 0.001). Women in winter have significantly elevated OR of 5.00 (95%CI 1.75–14.25) to develop vitamin D deficiency. Seasonal variation in serum 25(OH)D levels was not present in non-working individuals and women aged 31–44 years.ConclusionsVitamin D deficiency is common among preconception women especially nulliparous women and working women, which propose to screen serum 25(OH)D on preconception evaluation and emphasize need vitamin D supplements and get sunshine exposure.

Neurofibromatosis type I: points to be considered by general pediatricians.

Neurofibromatosis type 1 (NF1), a prevalent genetic disease that is transmitted in an autosomal dominant manner, is characterized by multiple cutaneous café-au-lait spots and neurofibromas as well as various degrees of neurological, skeletal, and neoplastic manifestations. The clinical features of NF1 increase in frequency with age, while the clinical diagnosis can remain undetermined in some pediatric patients. Importantly, affected patients are at risk for developing tumors of the central and peripheral nervous system. Therefore, adequate counseling for genetic testing, age-appropriate surveillance, and management are important. This review suggests several issues that should be considered to help general pediatricians provide adequate clinical care and genetic counseling to patients with NF1 and their families.

Clinical characteristics and variant analysis of five pedigrees with hereditary spastic paraplegia

To explore the clinical and genetic characteristics of five pedigrees affected with hereditary spastic paraplegia(HSP). Clinical data of the five pedigrees was collected, and high-throughput sequencing was carried out to detect potential variants. Sanger sequencing were used to verify the results. The probands of pedigree 1 and 2 were found to harbor heterozygous SPAST gene variants, namely c.1196C>T and c.1523T>A. The proband of pedigree 3 harbored compound heterozygous variants of FA2H gene (c.61G>C and c.688G>A). Proband from pedigree 4 harbored compound heterozygous variants of SPG11 gene (c.6812+4_6812+7delAGTA and c.915delT). The proband of pedigree 5 harbored compound heterozygous variants of SPG7 gene (c.1703_1704delAG and c.1937-1G>C). Based on the American College of Medical Genetics and Genomics(ACMG) guidelines, all variants were predicted to be likely pathogenic. Among these, SPAST gene c.1523T>A, FA2H gene c.61.G>C, SPG11 gene splicing region c.6812+4_6812+7delAGTA, c.915delT, SPG7 gene c.1703_1704delAG and splicing region c.1937-1G>C variants were unreported previously. The probands of pedigrees 1 and 2 were diagnosed with autosomal dominant hereditary spastic paraplegia type 4, for which pedigree 2 showed incompletely penetrance. Pedigrees 3, 4, and 5 were diagnosed with autosomal recessive hereditary spastic paraplegia type 35, 11 and 7, respectively. Above result provided a reference for clinical diagnosis and genetic counseling for the affected pedigrees.

Mutation Screening of mtDNA Combined Targeted Exon Sequencing in a Cohort With Suspected Hereditary Optic Neuropathy.

PurposeLeber hereditary optic neuropathy (LHON) and autosomal dominant optic atrophy (ADOA) are the two commonest forms of hereditary optic neuropathy. The aim of this study was to comprehensively investigate the incidence and spectrum of mutations in patients with suspected hereditary optic neuropathy by combining mitochondrial DNA (mtDNA) genome-wide and targeted exon sequencing.MethodsA cohort of 1101 subjects were recruited to participate in the study, comprising 177 families (177 probands and their family members, a total of 537 subjects, including 254 patients) and 164 sporadic cases with suspected hereditary optic neuropathy, and 400 unrelated control subjects for genetic analysis: all subjects (including control subjects) underwent a comprehensive ophthalmologic examination and were subjected to sequencing analysis of mtDNA genome-wide and targeted exon. Overall, targeted exon sequencing was used to screen 792 genes associated with common hereditary eye diseases, and the mtDNA genome-wide were screened by next-generation sequencing.ResultsWe found variants detected in 168 (40.2%, 168/418) of the 418 patients screened. Among these, 132 cases (78.6%, 132/168) were detected with known LHON disease-causing mtDNA variants; 40 cases (23.8%, 40/168) were detected with nuclear DNA (ntDNA) variants, which included 36 cases (21.4%, 36/168) with detected OPA1 mutations, 4 patients (2.4%, 4/168) with detected OPA3 mutations, and 2 patients (1.2%, 2/168) with detected TMEM126A homozygous mutation. Coexistence variation (mtDNA/mtDNA [n = 16], ntDNA/ntDNA [n = 4], mtDNA/ntDNA [n = 7]) was found in 27 patients (16.4%, 27/165), including mtDNA/ntDNA coexistence variation that was detected in seven patients. Among these ntDNA mutations, 38 distinct disease-causing variants, including autosomal recessive heterozygous mutations, were detected, which included 22 novel variants and two de novo variants. Total haplogroup distribution showed that 34.5% (29/84) and 28.6% (24/84) of the affected subjects with m.11778G>A belonged to haplogroup D and M, with a high frequency of subhaplogroups D4, D5, and M7.ConclusionsThe LHON-mtDNA mutations are the commonest genetic defects in this Chinese cohort, followed by the OPA1 mutations. To our knowledge, this is the first comprehensive study of LHON, ADOA, and autosomal recessive optic atrophy combined with mtDNA genome-wide and targeted exon sequencing, as well as haplogroup analysis, in a large cohort of Chinese patients with suspected hereditary optic neuropathy. Our findings provide a powerful basis for genetic counseling in patients with suspected hereditary optic neuropathy.Translational RelevanceWe applied mtDNA genome-wide sequencing combined with panel-based targeted exon sequencing to explore the pathogenic variation spectrum and genetic characteristics of patients with suspected hereditary optic neuropathy, providing a comprehensive research strategy for clinical assistant diagnosis, treatment, and genetic counseling.