The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy.
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ABSTRACT:
SUBMITTER: Pehlivan D
PROVIDER: S-EPMC5322766 | biostudies-literature | 2016 May
REPOSITORIES: biostudies-literature
Publications
The role of combined SNV and CNV burden in patients with distal symmetric polyneuropathy.
Pehlivan Davut D Beck Christine R CR Okamoto Yuji Y Harel Tamar T Akdemir Zeynep H C ZH Jhangiani Shalini N SN Withers Marjorie A MA Goksungur Meryem Tuba MT Carvalho Claudia M B CM Czesnik Dirk D Gonzaga-Jauregui Claudia C Wiszniewski Wojciech W Muzny Donna M DM Gibbs Richard A RA Rautenstrauss Bernd B Sereda Michael W MW Lupski James R JR
Genetics in medicine : official journal of the American College of Medical Genetics 20150917 5
<h4>Purpose</h4>Charcot-Marie-Tooth (CMT) disease is a heterogeneous group of genetic disorders of the peripheral nervous system. Copy-number variants (CNVs) contribute significantly to CMT, as duplication of PMP22 underlies the majority of CMT1 cases. We hypothesized that CNVs and/or single-nucleotide variants (SNVs) might exist in patients with CMT with an unknown molecular genetic etiology.<h4>Methods</h4>Two hundred patients with CMT, negative for both SNV mutations in several CMT genes and ...[more]
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Project description:Peripheral neuropathy is a common neurologic disorder, affecting 2% to 8% of the population in population-based studies with confirmation by neurologist examination. These prevalence numbers are remarkably stable across developed countries. In 1999, 8.6% of Medicare beneficiaries had neuropathy as a primary or secondary diagnosis, and the cost of treatment was estimated at $3.5 billion (Consumer Price Index adjusted to 2013 $4.9 billion), which did not include outpatient medications. Peripheral neuropathy has many causes and varies in regard to its clinical manifestations and severity. Distal symmetric polyneuropathy (DSP) is the most common pattern of peripheral neuropathy generally and the most common phenotype of neuropathy due to diabetes. Reported prevalence rates of DSP among diabetic patients range from 15% to 37% across large population-based studies, and the prevalence among those with impaired glucose tolerance has been reported to be 11%. DSP can result in weakness, sensory loss, pain, autonomic dysfunction, gait impairment, falls, disability, and impaired quality of life.
| S-EPMC4032209 | biostudies-literature
Project description:BackgroundDistal symmetric polyneuropathy (DSPN) is a common microvascular complication of both type 1 and 2 diabetes with substantial morbidity burden and reduced quality of life. Its association with mortality is equivocal.PurposeTo describe the association between DSPN and all-cause mortality in people with diabetes and further stratify by the type of diabetes based on a meta-analysis of published observational studies.Data sourcesWe searched Medline from inception to May 2021.Study selectionOriginal data were collected from case-control and cohort studies that reported on diabetes and DSPN status at baseline and all-cause mortality during follow-up.Data extractionwas completed by diabetes specialists with clinical experience in neuropathy assessment.Data synthesisData was synthesized using random-effects meta-analysis. The difference between type 1 and 2 diabetes was investigated using meta-regression.ResultsA total of 31 cohorts (n=155,934 participants, median 27.4% with DSPN at baseline, all-cause mortality 12.3%) were included. Diabetes patients with DSPN had an almost twofold mortality (HR: 1.96, 95%CI: 1.68-2.27, I2 = 91.7%), I2 = 91.7%) compared to those without DSPN that was partly explained by baseline risk factors (adjusted HR: 1.60, 95%CI: 1.37-1.87, I2 = 78.86%). The association was stronger in type 1 compared to type 2 diabetes (HR: 2.22, 95%CI: 1.43-3.45). Findings were robust in sensitivity analyses without significant publication bias.LimitationsNot all papers reported multiple adjusted estimates. The definition of DSPN was heterogeneous.ConclusionsDSPN is associated with an almost twofold risk of death. If this association is causal, targeted therapy for DSPN could improve life expectancy of diabetic patients.
| S-EPMC9978416 | biostudies-literature
Project description:Rationale: Physical exercise is an essential adjunct to the management of patients with type 2 diabetes mellitus. Therapeutic interventions that improve blood flow to peripheral nerves, such as exercise, may slow the progression of neuropathy in the diabetic patient. Aims: This randomized clinical trial was conducted to determine whether a structured program of aerobic, isokinetic strength, or the combination of aerobic-isokinetic strength exercise intervention alters peripheral nerve function in glycemic-controlled diabetic patients with advanced length-dependent distal symmetric polyneuropathy. Methods: Forty-five patients with type 2 diabetes mellitus exhibiting tight glycemic control (HbA1c intergroup range 7.2-8.0%) were randomized by block design across four experimental groups: sedentary controls (n = 12), aerobic exercise (n = 11), isokinetic strength (n = 11), or the combination of aerobic-isokinetic strength training (n = 11). Patients randomized to training groups exercised 3× per week for 12 weeks, whereas patients randomized to the sedentary control group received standard of care. To minimize attention and educational bias, all patients attended a 12-session health promotion educational series. At baseline, immediately following intervention, and again at 12-week post-intervention, detailed nerve conduction studies were conducted as a primary outcome measure. At these same intervals, all patients completed as secondary measures quantitative sensory testing, symptom-limited treadmill stress tests, and a Short-Form 36-Veterans Questionnaire (SF-36V). Results: Of the 45 patients randomized into this study, 37 (82%) had absent sural nerve responses, 19 (42%) had absent median sensory nerve responses, and 17 (38%) had absent ulnar sensory nerve responses. By comparison, responses from tibial nerves were absent in only three (7%) subjects while responses from peroneal nerves were absent in five (11%) subjects. Eleven (92%) of 12 patients that had volunteered to be biopsied exhibited abnormal levels of epidermal nerve fiber densities. Exercise, regardless of type, did not alter sensory or motor nerve electrodiagnostic findings among those patients exhibiting measurable responses (ANOVA). There was, however, a modest (p = 0.01) beneficial effect of exercise on sensory nerve function (Fisher's Exact Test). Importantly, the beneficial effect of exercise on sensory nerve function was enhanced (p = 0.03) during the post-intervention interval. In addition, three of six patients that had undergone exercise intervention exhibited a marked 1.9 ± 0.3-fold improvement in epidermal nerve fiber density. By comparison, none of three sedentary patients whom agreed to be biopsied a second time showed improvement in epidermal nerve fiber density. Compared to baseline values within groups, and compared with sedentary values across groups, neither aerobic, isokinetic strength, or the combination of aerobic-isokinetic strength exercise intervention altered peak oxygen uptake. Patients that underwent aerobic or the combined aerobic-isokinetic strength exercise intervention, however, demonstrated an increase in treadmill test duration that was sustained over the 12-week post-intervention period. Conclusion: A 12-week course of physical exercise, regardless of type, does not alter sensory or motor nerve electrodiagnostic findings. In a subset of patients, a short-term structured program of aerobic exercise may selectively improve sensory nerve fiber function. Large-scale exercise lifestyle intervention trials are warranted to further evaluate the impact of aerobic exercise on sensory nerve fiber function in diabetic neuropathic patients. Clinical Trial Registration: www.ClinicalTrials.gov, identifier NCT00955201.
| S-EPMC6379046 | biostudies-literature
Project description:ObjectiveTo estimate the accuracy of Neuropad for the diagnosis and staging of distal symmetric polyneuropathy (DPN) across different stages of neuropathy, using multiple-level likelihood ratios (LRs) to interpret the time necessary to complete the color change of the test.Research design and methodsWe conducted a cross-sectional, cohort-type diagnostic accuracy study in 251 consecutive adult type 2 diabetic patients with no peripheral arterial disease or other potential causes of neuropathy, who were recruited between January 2005 and December 2008 from the diabetes outpatient clinics in Alexandroupolis Hospital, Greece. Patients were tested for DPN by means of the neuropathy disability score (NDS) and Neuropad. Multiple-level LRs for time to complete color change were calculated across different stages of neuropathy.ResultsThe areas under the curve for the diagnosis of any (NDS of ?3), at least moderate (NDS of ?6), or severe (NDS of ?9) DPN were 0.91, 0.96, and 0.97, respectively. The calculation of multiple-level LRs showed that time to complete color change <360 s suggested the absence of neuropathy. Values between 360 and 1,000 s were indicative of mild neuropathy. Finally, values between 1,000 and 1,200 or >1,200 s were strongly suggestive of moderate or severe DPN, respectively.ConclusionsNeuropad could be used as a triage test for the diagnosis and staging of DPN in patients with type 2 diabetes, prompting referral to specialized care setting.
| S-EPMC3114325 | biostudies-literature
Project description:BackgroundPeople with diabetic cardiovascular autonomic neuropathy (CAN) have increased cardiovascular mortality. However, the association between distal symmetric polyneuropathy (DSPN) or CAN with all-cause mortality is much less investigated. Thus, we set out to examine the effect of CAN and DSPN on all-cause mortality in a well-phenotyped cohort.MethodsAll diabetes cases (n = 1,347) from the catchment area of a secondary diabetes care centre who had medical examination including neuropathy assessment between 1997 and 2016 were followed up for all-cause mortality in the NHS Hungary reimbursement database until 2018. We investigated the association of CAN (Ewing tests) and DSPN (Neurometer) with all-cause mortality using Cox models stratified by diabetes type.ResultsAltogether, n = 131/1,011 persons with type 1/type 2 diabetes were included. Of the participants, 53%/43% were male, mean age was 46 ± 12/64 ± 10 years, diabetes duration was 13 ± 10/7 ± 8 years, 42%/29% had CAN, and 39%/37% had DSPN. During the 9 ± 5/8 ± 5-year follow-up, n = 28/494 participants died. In fully adjusted models, participants with type 1 diabetes patients with versus without DSPN had an increased mortality (HR 2.99, 95% CI 1.4-8.63), while no association with CAN was observed. In type 2 diabetes, both DSPN and CAN independently increased mortality (HR 1.32, 95% CI: 1.07-1.64, and HR 1.44, 95% CI: 1.17-1.76).ConclusionsOur results are compatible with an increased risk of mortality in people with type 1 diabetes and DSPN. Furthermore, we report a similarly strong association between DSPN and CAN and all-cause mortality in type 2 diabetes mellitus.
| S-EPMC8181184 | biostudies-literature
Project description:BACKGROUND:Diabetic distal symmetric polyneuropathy (DSPN) is one of the most common microvascular complications of diabetes mellitus, and it has become a major public health problem worldwide because of its high and increasing prevalence, morbidity, and disability rate. The current medications for DSPN are not entirely satisfactory. Preliminary studies indicated that the Chinese herbal TangBi Formula may alleviate signs and symptoms and improve the velocity of nerve conduction in patients with DSPN. This study was designed to determine if Chinese herbal medicine used in combination with conventional treatment is more effective than conventional treatment alone. METHODS/DESIGN:We are conducting a multicenter, placebo-controlled, double-blind, randomized, controlled clinical trial as a means of assessing the therapeutic effects of traditional Chinese medicine (TCM) treatment. A total of 188 patients will be randomized in a 1:1 ratio to a treatment group (TangBi Formula plus mecobalamin) and a control group (placebo plus mecobalamin). The test period lasts 6 months, during which all of the patients will be given standard medical care as recommended by established guidelines. The primary outcome will be development of differences in changes in clinical symptoms and signs in patients and changes in Michigan Diabetic Neuropathy Score (MDNS) between the two groups before and after treatment. The secondary outcome will be changes in nerve conduction velocity and in single clinical signs and symptoms. Safety assessments and adverse events will also be evaluated. DISCUSSION:We postulate that patients with DSPN will benefit from therapy that includes TCM. If successful, this work will provide an evidence-based complementary therapeutic approach for treatment of DSPN. TRIAL REGISTRATION:ClinicalTrials.gov, NCT03010241 . Registered on 2 January 2017.
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Project description:Male factor infertility affects about 7% of men in the general population and it can be related to a number of different etiologic factors, including genetic anomalies. Both sex chromosomes are enriched in genes prevalently or exclusively expressed in the testis. Nevertheless only the Y chromosome-linked Copy Number Variants (CNVs) and Y-linked genes have been demonstrated as important contributors to impaired sperm production in humans Data on the potential role of X-linked gene products in spermatogenesis derives mainly from model organisms. X-linked genes seem to be expressed both in pre-meiotic and post-meiotic germ cells in the mouse testis and interestingly those expressed in the post-meiotic cells belong to multicopy gene families. The apparent paucity of X-linked factors in male infertility is most likely related to the scarcity of studies, which focused only on a total of seven genes. No pathogenic mutations causing infertility have, thus far, been described in these genes, with the exception of AR gene In order to advance in the understanding of the role of X-linked CNVs and genes in male infertility, we applied an innovative approach based on high resolution X chromosome specific CGH array. Given that such a detailed analysis of the X chromosome has not been published so far and the testicular function of subjects included in the Genomic Variant Database is unknown (except for 24 X-linked CNVs reported in the recent paper by Tuttelmann), our is the first study providing a detailed analysis of X-linked losses and gains in several hundreds of subjects with known sperm parameters. The study was approved by the local Ethical Committees of the University Hospital Careggi (Italy) and the Fundacio Puigvert (Spain). All participants signed an informed consent. 96 infertile subjects with different grade of spermatogenic impairment (74 azoospermic, 6 mild oligozoospermia and 16 severe oligozoospermic men) and 103 normozoospermic men have been analyzed with aCGH. All known causes of impaired spermatogenesis have been excluded in the patients and testis histology was available for 47 men. The ethnic composition was similar in the controls and patients groups (40% Spanish and 60% Italians). A customized array-CGH platform (custom 8 x 60K, Agilent Technologies) was generated using the eArray software (http://earray.chem.agilent.com/); probes, selected from those available in the Agilent database, covered the whole X chromosome, including Xp and Xq pseudoregions, with an average resolution of 4 Kb. As a reference DNA, we used the same normozoospermic subject for the entire study population. This control DNA was already characterized for CNV content in previous array-CGH experiments against different (8) normospermic controls. In the second part of the study, we performed a case-control study on 31 selected CNVs which appeared to be specific for infertile men after the aCGH analysis. For these selected losses a total of 359 patients and 370 normozoospermic controls were studied. With regard to the gains, 270 patients and 325 controls were analyzed (further phenotypic data are provided in supplementary tables 1a-e). Deletions were analyzed by PCR plus/minus, whereas loss 31 and all the gains have been analyzed with Real Time PCR using TaqMan Copy Number Assay. CNV code Loss or Gain Region Size (kb) Start End 1a GAIN Xp22.33 224,83 1544 226372 4.A GAIN Xp22.33 237,08 153373 390452 5 GAIN Xp22.33 160,10 302644 462740 5.A GAIN Xp22.33 241,98 674222 916206 5.B LOSS Xp22.33 12,63 701071 713696 5.C GAIN Xp22.33 420,72 747358 1168080 11 GAIN Xp22.33 39,73 1347599 1387328 12 GAIN Xp22.33 17,30 1693897 1711194 12.A GAIN Xp22.33 6,61 1693897 1700511 12.B GAIN Xp22.33 683,74 1716023 2399766 14 GAIN Xp22.33 1,40 1896197 1897608 15 LOSS Xp22.33 1,40 1896197 1897608 15.A GAIN Xp22.33 27,94 2382699 2410643 15.B GAIN Xp22.33/22.32 280,09 4206493 4486580 16 LOSS Xp22.32 7,76 4250413 4258174 16.A GAIN Xp22.31 1609,42 6487238 8096662 17 LOSS Xp22.31 31,70 6594834 6626533 18 LOSS Xp22.31 82,00 6756310 6838310 19 GAIN Xp22.31 245,03 7002649 7247676 19.A GAIN Xp22.31 129,96 7961788 8091751 19.B GAIN Xp22.31 177,54 8411159 8588699 20 GAIN Xp22.2 602,10 11104518 11706614 20.A GAIN Xp22.2 665,88 14590604 15256487 20.B GAIN Xp22.13 13,34 18018894 18032238 22 LOSS Xp22.11 24,35 22969648 22993997 23 LOSS Xp21.3 6,69 25274024 25280712 24 LOSS Xp21.3 67,33 26891769 26959101 25 GAIN Xp21.3 60,40 27277529 27337933 25.A LOSS Xp21.2 9,69 31282923 31292613 25.B LOSS Xp21.1 28,26 33953232 33981492 25.C GAIN Xp21.1 185,02 34931807 35116827 25.D GAIN Xp21.1 215,00 35269628 35484626 26 GAIN Xp21.1 88,57 37168387 37256960 27 GAIN Xp21.1 9,61 37242364 37251969 30 GAIN Xp11.3 81,13 47766391 47847516 31 LOSS Xp11.3 81,13 47766391 47847516 31.A GAIN Xp11.23 78,87 48021982 48100848 32 LOSS Xp11.22 4,15 52065798 52069943 33.A LOSS Xp11.21 58,89 56403390 56462278 34.A GAIN Xp11.12 48,06 56870427 56918489 35 GAIN Xp11.1 117,14 57318438 57435573 36.A GAIN Xq11 716,03 63925948 64641977 38 GAIN Xq13.2 8,98 72202996 72211976 38.A GAIN Xq13.2 192,04 74375875 74567915 38.B GAIN Xq13.3 153,23 75123387 75276621 39 GAIN Xq21.1 21,98 76992067 77014050 40 GAIN Xq21.1 5,28 80112246 80117526 49 GAIN Xq22.1 5,30 100942190 100947490 50 LOSS Xq22.1 45,36 101803578 101848935 51 GAIN Xq22.2 34,69 103152319 103187013 53.A LOSS Xq24 170,73 118278913 118449646 54 LOSS Xq24 44,85 118281024 118325874 55 GAIN Xq24 206,90 118691020 118897917 55.A GAIN Xq25 53,80 120385787 120439584 56 LOSS Xq25 86,07 124632886 124718959 57 LOSS Xq25 188,03 124929673 125117699 58 GAIN Xq25 9,68 125143278 125152957 58.A LOSS Xq25 12,68 125198109 125210792 59.A GAIN Xq26.3 24,69 134151039 134175725 60 GAIN Xq26.3 42,30 134585636 134627936 60.A LOSS Xq26.3 50,84 134801361 134852198 60.B GAIN Xq26.3 13,45 136050422 136063872 60.C GAIN Xq26.3 91,26 137089527 137180783 60.D LOSS Xq27.1 217,83 140175103 140392930 61 LOSS Xq27.2 4,67 140773893 140778561 64 LOSS Xq27.3 3,92 143436347 143440268 66 LOSS Xq27.3 7,35 145030566 145037917 66.A LOSS Xq28 37,12 147393583 147430698 67 LOSS Xq28 5,42 148456474 148461889 68 GAIN Xq28 105,66 148686631 148792286 69 LOSS Xq28 11,77 154044877 154056645 71 LOSS Xq28 290,99 154586913 154877901 71.A LOSS Xq28 122,36 154755542 154877901
2012-10-01 | E-GEOD-37948 | biostudies-arrayexpress
Project description:Compared with the general population, an excess of rare copy number variants (CNVs) has been identified in people with schizophrenia. Females with neurodevelopmental disorders and in the general population have been reported to carry more large, rare CNVs than males. Given that many schizophrenia datasets do not have equal gender ratios in cases and controls, sex differences in CNV burden might have impacted on estimates of case-related CNV burden and also on associations to individual loci. In a sample of 13,276 cases and 17,863 controls, we observed a small but significant excess of large (≥500 Kb), rare (<1%) CNVs in females compared with males in both cases and controls (OR = 1.17, P = 0.0012 for controls; OR = 1.11, P = 0.045 for cases). The burden of 11 schizophrenia-associated CNVs was significantly higher in female cases compared with male cases (OR = 1.38, P = 0.0055), but after accounting for the rates of CNVs in controls, we found no significant gender difference in the risk conferred by these loci. Controlling for gender had a negligible effect on the significance of association between specific CNVs and schizophrenia. The female excess of large CNVs in both cases and controls suggests a female protective mechanism exists for deleterious CNVs that may extend beyond neurodevelopmental phenotypes.
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Project description:Male factor infertility affects about 7% of men in the general population and it can be related to a number of different etiologic factors, including genetic anomalies. Both sex chromosomes are enriched in genes prevalently or exclusively expressed in the testis. Nevertheless only the Y chromosome-linked Copy Number Variants (CNVs) and Y-linked genes have been demonstrated as important contributors to impaired sperm production in humans Data on the potential role of X-linked gene products in spermatogenesis derives mainly from model organisms. X-linked genes seem to be expressed both in pre-meiotic and post-meiotic germ cells in the mouse testis and interestingly those expressed in the post-meiotic cells belong to multicopy gene families. The apparent paucity of X-linked factors in male infertility is most likely related to the scarcity of studies, which focused only on a total of seven genes. No pathogenic mutations causing infertility have, thus far, been described in these genes, with the exception of AR gene In order to advance in the understanding of the role of X-linked CNVs and genes in male infertility, we applied an innovative approach based on high resolution X chromosome specific CGH array. Given that such a detailed analysis of the X chromosome has not been published so far and the testicular function of subjects included in the Genomic Variant Database is unknown (except for 24 X-linked CNVs reported in the recent paper by Tuttelmann), our is the first study providing a detailed analysis of X-linked losses and gains in several hundreds of subjects with known sperm parameters.
2012-10-01 | GSE37948 | GEO
Project description:High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations, and provides a critical resource that can be used to more accurately identify pathogenic genetic variants. We report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project when prioritizing disease-causing variants. KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations.
| S-EPMC5885007 | biostudies-literature