Allele Length Research Articles

Loss of Corneal Nerves and Corneal Haze in Patients with Fuchs’ Endothelial Corneal Dystrophy with the Transcription Factor 4 Gene Trinucleotide Repeat Expansion

ObjectiveSeventy percent of Fuchs’ endothelial corneal dystrophy (FECD) cases are caused by an intronic trinucleotide repeat expansion in the transcription factor 4 gene (TCF4). The objective of this study was to characterize the corneal subbasal nerve plexus and corneal haze in patients with FECD with (RE+) and without the trinucleotide repeat expansion (RE−) and to assess the correlation of these parameters with disease severity.DesignCross-sectional, single-center study.ParticipantsFifty-two eyes of 29 subjects with a modified Krachmer grade of FECD severity from 1 to 6 were included in the study. Fifteen of the 29 subjects carried an expanded TCF4 allele length of ≥ 40 cytosine-thymine-guanine repeats (RE+).Main Outcomes MeasuresIn vivo confocal microscopy assessments of corneal nerve fiber length (CNFL), corneal nerve branch density, corneal nerve fiber density (CNFD), and anterior corneal stromal backscatter (haze); Scheimpflug tomography densitometry measurements of haze in anterior, central, and posterior corneal layers.ResultsUsing confocal microscopy, we detected a negative correlation between FECD severity and both CNFL and CNFD in the eyes of RE+ subjects (Spearman ρ = −0.45, P = 0.029 and ρ = −0.62, P = 0.0015, respectively) but not in the eyes of RE− subjects. Additionally, CNFD negatively correlated with the repeat length of the expanded allele in the RE+ subjects (Spearman ρ = −0.42, P = 0.038). We found a positive correlation between anterior stromal backscatter and severity in both the RE+ and RE− groups (ρ = 0.60, P = 0.0023 and ρ = 0.44, P = 0.024, respectively). The anterior, central, and posterior Scheimpflug densitometry measurements also positively correlated with severity in both the RE+ and RE− groups (P = 5.5 × 10−5, 2.5 × 10−4, and 2.9 × 10−4, respectively, after adjusting for the expansion status in a pooled analysis. However, for patients with severe FECD (Krachmer grades 5 and 6), the posterior densitometry measurements were higher in the RE+ group than in the RE− group (P < 0.05).ConclusionsLoss of corneal nerves in FECD supports the classification of the TCF4 trinucleotide repeat expansion disorder as a neurodegenerative disease. Haze in the anterior, central, and posterior cornea correlate with severity, irrespective of the genotype. Quantitative assessments of corneal nerves and corneal haze may be useful to gauge and monitor FECD disease severity in RE+ patients.

MUC5B, telomere length and longitudinal quantitative interstitial lung changes: the MESA Lung Study

BackgroundThe MUC5B promoter variant (rs35705950) and telomere length are linked to pulmonary fibrosis and CT-based qualitative assessments of interstitial abnormalities, but their associations with longitudinal quantitative changes of the lung...

The repeat length of C9orf72 is associated with the survival of amyotrophic lateral sclerosis patients without C9orf72 pathological expansions

ObjectiveTo explore whether the repeat lengths of the chromosome 9 open reading frame 72 (C9orf72) gene and the ataxin-2 (ATXN2) gene in amyotrophic lateral sclerosis (ALS) patients without C9orf72 repeat expansions confer a risk of ALS or survival disadvantages in ALS.MethodsWe screened a hospital-based cohort of Chinese patients with sporadic ALS without C9orf72 repeat expansions and neurologically healthy controls for C9orf72 GGGGCC and AXTN2 CAG repeat length to compare the frequency of possible detrimental length alleles using several thresholds. Furthermore, the clinical features of ALS were compared between patients with ALS subgroups using different length thresholds of maximum C9orf72 and ATXN2 repeat alleles, such as sex, age of onset, diagnostic delay, and survival.ResultsOverall, 879 sporadic patients with ALS and 535 controls were included and the repeat lengths of the C9orf72 and ATXN2 were both detected. We found significant survival differences in patients using a series of C9orf72 repeat length thresholds from 2 to 5, among which the most significant difference was at the cutoff value of 2 (repeats 2 vs. >2: median survival 67 vs. 55 months, log-rank p = 0.032). Furthermore, Cox regression analysis revealed the role of age of onset [hazard ratio (HR) 1.04, 95% CI 1.03–1.05, p < 0.001], diagnostic delay (0.95, 0.94–0.96, p < 0.001), and carrying C9orf72 repeat length of 2 (0.72, 0.59–0.89, p = 0.002) in the survival of patients without C9orf72 repeat expansions. In addition, bulbar onset was associated with poorer survival when the patients carried the maximum C9orf72 repeat allele over 2 (1.81, 1.32–2.48, p < 0.001). However, no survival difference was found when applying a series of continuous cutoff values of ATXN2 or stratified by C9orf72 repeats of 2.ConclusionThe length of 2 in the maximum C9orf72 repeat allele was identified to be associated with favorable survival in ALS patients without C9orf72 repeat expansions. Our findings from the clinical setting implicated the possible cutoff definition of detrimental C9orf72 repeats, which should be helpful in the understanding of genetics in ALS and in clinical genetic counseling.

The Natural History of Spinocerebellar Ataxia Type 3 in Mainland China: A 2-Year Cohort Study.

ObjectiveThe natural history of spinocerebellar ataxia type 3 (SCA3) has been reported in several populations and shows heterogeneity in progression rate and affecting factors. However, it remains unexplored in the population of Mainland China. This study aimed to identify the disease progression rate and its potential affecting factors in patients with SCA3 in Mainland China.Participants and MethodsWe enrolled patients with genetically confirmed SCA3 in Mainland China. Patients were seen at three visits, i.e., baseline, 1 year, and 2 years. The primary outcome was the Scale for the Assessment and Rating of Ataxia (SARA), and the secondary outcomes were the Inventory of Non-Ataxia Signs (INAS) as well as the SCA Functional Index (SCAFI).ResultsBetween 1 October 2015, and 30 September 2016, we enrolled 263 patients with SCA3. We analyzed 247 patients with at least one follow-up visit. The annual progression rate of SARA was 1.49 points per year (SE 0.08, 95% confidence interval [CI] 1.33–1.65, p < 0.0001). The annual progression rates of INAS and SCAFI were 0.56 points per year (SE 0.05, 95% CI 0.47–0.66, p < 0.001) and −0.30 points per year (SE 0.01, 95% CI −0.33∼-0.28, p < 0.001), respectively. Faster progression in SARA was associated with longer length of the expanded allele of ATXN3 (p < 0.0001); faster progression in INAS was associated with lower INAS at baseline (p < 0.0001); faster decline in SCAFI was associated with shorter length of the normal allele of ATXN3 (p = 0.036) and higher SCAFI at baseline (p < 0.0001).ConclusionOur results provide quantitative data on the disease progression of patients with SCA3 in Mainland China and its corresponding affecting factors, which could facilitate the sample size calculation and patient stratification in future clinical trials.Trial RegistrationThis study was registered with Chictr.org on 15 September 2015, number ChiCTR-OOC-15007124.

A comparative study of population genetic structure reveals patterns consistent with selection at functional microsatellites in common sunflower.

Microsatellites, also known as short tandem repeats (STRs), have long been considered non-functional, neutrally evolving regions of the genome. Recent findings suggest that they can function as drivers of rapid adaptive evolution. Previous work on the common sunflower identified 479 transcribed microsatellites where allele length significantly correlates with gene expression (eSTRs) in a stepwise manner. Here, a population genetic approach is used to test whether eSTR allele length variation is under selection. Genotypic variation among and within populations at 13 eSTRs was compared with that at 19 anonymous microsatellites in 672 individuals from 17 natural populations of sunflower from across a cline running from Saskatchewan to Oklahoma (distance of approximately 1600km). Expected heterozygosity, allelic richness, and allelic diversity were significantly lower at eSTRs, a pattern consistent with higher relative rates of purifying selection. Further, an analysis of variation in microsatellite allele lengths (lnRV), and heterozygosities (lnRH), indicate recent selective sweeps at the eSTRs. Mean microsatellite allele lengths at four eSTRs within populations are significantly correlated with latitude consistent with the predictions of the tuning-knob model which predicts stepwise relationships between microsatellite allele length and phenotypes. This finding suggests that shorter or longer alleles at eSTRs may be favored in climatic extremes. Collectively, our results imply that eSTRs are likely under selection and that they may be playing a role in facilitating local adaptation across a well-defined cline in the common sunflower.

Characterization of 58 STRs and 94 SNPs with the ForenSeq™ DNA signature prep kit in Mexican-Mestizos from the Monterrey city (Northeast, Mexico).

STR allele frequency databases from populations are necessary to take full advantage of the increased power of discrimination offered by massively parallel sequencing (MPS) platforms. For this reason, we sequenced 58 STRs (aSTRs, X-STRs, and Y-STRs) and 94 identity informative SNPs (iiSNPs) on 105 Mestizo (admixed) individuals from Monterrey City (Northeast, Mexico), with the Primer Set-A of the ForenSeq™ DNA Signature Prep Kit. Most of the STR markers were in Hardy Weinberg equilibrium, with a few exceptions. We found 346 different length-based alleles for these 58 STRs; nevertheless, they became 528 alleles when the sequence was assessed. The combined power of discrimination from autosomal STRs (aSTRs) was -virtually- 100% in both length and sequence-based alleles, while the power of exclusion was 99.9999999976065 and 99.9999999999494%, respectively. Haplotypes based on X-STRs and Y-STRs showed 100% of discriminatory capacity. These results provide -for the first time- forensic genomic population data from Mexico necessary for interpretation in kinship and criminal analyses.

Sequencing of autosomal, mitochondrial and Y-chromosomal forensic markers in the People of the British Isles cohort detects population structure dominated by patrilineages

Short tandem repeat (STR) polymorphisms are traditionally assessed by measuring allele lengths via capillary electrophoresis (CE). Massively parallel sequencing (MPS) reveals differences among alleles of the same length, thus improving discrimination, but also identifying groups of alleles likely related by descent. These may have relatively restricted geographical distributions and thus MPS could detect population structure more effectively than CE-based analysis. We addressed this question by applying an MPS multiplex, the Promega PowerSeq™ Auto/Mito/Y System prototype, to 362 individuals chosen to represent a wide geographical spread from the People of the British Isles (PoBI) cohort, which represents at least three generations of local rural ancestry. As well as 22 autosomal STRs (aSTRs; equivalent to PowerPlex Fusion loci) the system sequences 23 Y-STRs (the PowerPlexY 23 loci) and the control region (CR) of mitochondrial DNA (mtDNA), allowing population structure to be compared across biparentally and uniparentally inherited segments of the genome. For all loci, FST-based tests of population structure were done based on historical, linguistic, and geographical partitions, and for aSTRs the clustering algorithm STRUCTURE was also applied. STRs were considered using both length and sequence. Sequencing increased aSTR allele diversity by 87.5% compared to CE-based designations, reducing random match probability to 1.25E-30, compared to a CE-based 6.72E-27. Significant population structure was detectable in just one pairwise comparison (Central/South East England compared to the rest), and for sequence-based alleles only. The 362 samples carried 308 distinct mtDNA CR haplotypes corresponding to 13 broad haplogroups, representing a haplotype diversity of 0.9985 ( ± 0.0005), and a haplotype match probability of 0.0043. No significant population structure was observed. Y-STR haplotypes belonged to ten broad predicted Y-haplogroups. Allele diversity increased by 33% when considered at the sequence rather than length level, although haplotype diversity was unchanged at 0.999969 ( ± 0.000001); haplotype match probability was 2.79E-03. In contrast to the biparentally and maternally inherited loci, Y-STR haplotypes showed significant population structure at several levels, but most markedly in a comparison of regions subject to Anglo-Saxon influence in the east with the rest of the sample. This was evident for both length- and sequence-based allele designations, with no systematic difference between the two. We conclude that MPS analysis of aSTRs or Y-STRs does not generally reveal stronger population structure than length-based analysis, that UK maternal lineages are not significantly structured, and that Y-STR haplotypes reveal significant population structure that may reflect the Anglo-Saxon migrations to Britain in the 6th century.

Genetic Diversity and Population Structure of Bullet Tuna (Auxis rochei) from Bali and Its Adjacent Waters

Bullet tuna (Auxis rochei) dominates the neritic tuna catch, especially from the purse seine fleet within the western and southern Indonesian waters. However, high catches can lead to stock depletion and lower genetic diversity due to possible inbreeding. Therefore, population genetic information is important in monitoring the sustainability of fish stocks and proposing an appropriate species-specific conservation strategy. This study aimed to analyze the genetic diversity, population structure, and kinship relationship of bullet tuna in Bali and its adjacent waters. Sampling was carried out in September 2020 at landing sites/ports representing the north, east, south, and west region, whereas at least 30 samples were acquired at each location. The result showed that the DNA concentration obtained could produce DNA bands with allele length ranged from 94-260 bp. Observed heterozygosity (Ho) was around 0.440-0.627. While the expected heterozygosity (He) was between 0.932-0.945. The genetic variation among population, within-population, and individuals was 0.36%, 41.04%, and 58.60%, respectively. The results of the analysis of genetic diversity between individuals in the population showed very high genetic diversity. The population structure of the bullet tuna landed in West Bali, East Bali, South Bali and North Bali is the same population stock. The kinship relationship indicates that the four populations are closely related genetically.

Haplotype-specific insertion-deletion variations for allele-specific targeting in Huntington's disease

Huntington's disease (HD) is a dominantly inherited neurodegenerative disease caused by an expanded CAG repeat in huntingtin (HTT). Given an important role for HTT in development and significant neurodegeneration at the time of clinical manifestation in HD, early treatment of allele-specific drugs represents a promising strategy. The feasibility of an allele-specific antisense oligonucleotide (ASO) targeting single-nucleotide polymorphisms (SNPs) has been demonstrated in models of HD. Here, we constructed a map of haplotype-specific insertion-deletion variations (indels) to develop alternative mutant-HTT-specific strategies. We mapped indels annotated in the 1000 Genomes Project data on common HTT haplotypes, revealing candidate indels for mutant-specific HTT targeting. Subsequent sequencing of an HD family confirmed candidate sites and revealed additional allele-specific indels. Interestingly, the most common normal HTT haplotype carries indels of big allele length differences at many sites, further uncovering promising haplotype-specific targets. When patient-derived cells carrying the most common HTT diplotype were treated with ASOs targeting the mutant alleles of candidate indels (rs772629195 or rs72239206), complete mutant specificity was observed. In summary, our map of haplotype-specific indels permits the identification of allele-specific targets in HD subjects, potentially contributing to the development of safe HTT-lowering therapeutics that are suitable for early treatment in HD.

Molecular profile of FLT3-mutated relapsed/refractory patients with AML in the phase 3 ADMIRAL study of gilteritinib

AbstractThe phase 3 Study of ASP2215 Versus Salvage Chemotherapy in Patients With Relapsed or Refractory Acute Myeloid Leukemia (AML) With FMS-like Tyrosine Kinase (FLT3) Mutation (ADMIRAL) trial demonstrated the superiority of the FLT3 inhibitor, gilteritinib, to salvage chemotherapy (SC) in patients with FLT3-mutated relapsed or refractory (R/R) AML. Baseline comutations, FLT3-internal tandem duplication (ITD) allelic ratio and length, and treatment-emergent mutations were analyzed in patients in the ADMIRAL trial. Baseline comutations were grouped according to gene subgroups (DNA methylation/hydroxymethylation, transcription, chromatin–spliceosome, receptor tyrosine kinase-Ras signaling, TP53-aneuploidy, NPM1, DNMT3A, DNMT3A/NPM1, WT-1, and IDH1/IDH2). Across all but 1 gene subgroup (TP53-aneuploidy), higher pretransplant response rates and a trend toward longer overall survival were observed with gilteritinib vs SC. Patients with DNMT3A/NPM1 comutations who received gilteritinib had the most favorable outcomes of any molecular subgroup analyzed. Survival outcomes with gilteritinib were not adversely affected by FLT3-ITD allelic ratio, FLT3-ITD length, or multiple FLT3-ITD mutations. Among patients who relapsed on gilteritinib, Ras/mitogen-activated protein kinase (MAPK) pathway and FLT3 F691L gene mutations were the most common mutational events associated with treatment resistance. However, the occurrence of Ras/MAPK pathway gene mutations at baseline did not preclude a clinical benefit from gilteritinib. Acquisition of multiple Ras/MAPK pathway gene mutations at relapse suggests a high level of pathway reactivation is needed to overcome the gilteritinib treatment effect. These findings provide insight into the R/R AML molecular profile and the impact of FLT3 inhibitors on mutational evolution associated with treatment resistance and benefit of gilteritinib across a wide spectrum of molecular and genetic subgroups in FLT3-mutated R/R AML. This trial was registered at www.clinicaltrials.gov as #NCT02421939.

80. Heme Oxygenase-1 Gene promoter and associations with inflammation and subclinical vascular disease in Ugandan adolescents with and without HIV

Abstract Background Heme oxygenase-1 (HO-1) is a cytoprotective enzyme with potent anti-inflammatory, and anti-oxidant effects. The HO-1 response is modulated by functional polymorphisms (a dinucleotide (GT)n repeat length variation) in the HO-1 gene promoter region which have been associated with cardiovascular disease (CVD) susceptibility in adults. HO-1 polymorphisms and their associations with markers of inflammation and CVD in Ugandan adolescents with (HIV+) and without HIV (HIV-) have not been investigated. Methods We included 177 children (92 HIV+, 85 HIV-) enrolled in an ongoing observational cohort study at the Joint Clinical Research Center, Kampala, Uganda. All HIV+ participants were on ART. HO-1 (GT)n allele genotypes were determined by PCR of the (GT)n repeat region followed by fragment size determination on a capillary sequencer in DNA extracted from blood samples. Allele designations were assigned by number of (GT)n repeats: S &amp;lt; 27, M 27-34, or L &amp;gt; 34 repeats. We measured mean common carotid artery intima-media thickness (IMT) as a marker of CVD, markers of systemic inflammation (hsCRP, IL6, sTNFRI), monocyte activation (sCD14 and sCD163), and T-cell activation (expression of CD38 and HLA-DR on CD4+ and CD8+) , oxidized lipids, markers of gut integrity and fungal translocation (BDG). Results Median age (IQR) was 13 (11, 14), 44% were females, 86% had viral load &amp;lt; 20 copies/mL. 19% had a short allele genotype, 37% had a medium allele genotype and 44% had a long allele genotype (Figure). The shortest and longest allele length correlated with lower IMT in HIV- only (r=-0.36 and -0.30, respectively, p≤ 0.01 for both). Among biomarkers, only the medium allele correlated with oxidized lipids in HIV+ and with hsCRP and BDG in HIV- (p≤ 0.05). After adjusting for age, sex, and BMI, the presence of a long allele was associated with lower IMT. This was no longer significant after adjusting for markers of inflammation or oxidized lipids (Table). Heme Oxygenase-1 genotype allele length frequency in Ugandan cohort of HIV+ and HIV- youth 1: Models are adjusted for age (years), sex (male vs female), BMI (kg/m2) and HIV status (positive vs negative) 2: Models are adjusted for age (years), sex (male vs female), BMI (kg/m2), sCD14 (pg/mL) and HIV status (positive vs negative) 3: Models are adjusted for age (years), sex (male vs female), BMI (kg/m2), high sensitivity C reactive protein (ng/mL) and HIV status (positive vs negative) 4: Models are adjusted for age (years), sex (male vs female), BMI (kg/m2), oxidized lipids and HIV status (positive vs negative) Conclusion These findings underscore the potential of the HO pathways in modulating future risk for CVD in adolescents through inflammation. HIV status in this setting, likely influences the associations with the genotype with the risk of CVD. Further studies to validate our findings in this population are required. Disclosures Grace A. McComsey, MD, Gilead (Consultant, Advisor or Review Panel member)Janssen (Consultant, Advisor or Review Panel member)Merck (Consultant, Grant/Research Support, Scientific Research Study Investigator, Advisor or Review Panel member)Redhill (Research Grant or Support)Roche (Grant/Research Support)Tetraphase, Astellas (Research Grant or Support)Theratechnologies (Consultant)Vanda (Grant/Research Support)ViiV/GSK (Scientific Research Study Investigator, Advisor or Review Panel member)

Germline polymorphisms and alternative splicing of human immunoglobulin light chain genes

SummaryInference of germline polymorphisms in immunoglobulin genes from B cell receptor repertoires is complicated by somatic hypermutations, sequencing/PCR errors, and by varying length of reference alleles. The light chain inference is particularly challenging owing to large gene duplications and absence of D genes. We analyzed the light chain cDNA sequences from naïve B cell receptor repertoires from 100 individuals. We optimized light chain allele inference by tweaking parameters of the TIgGER functions, extending the germline reference sequences, and establishing mismatch frequency patterns at polymorphic positions to filter out false-positive candidates. We identified 48 previously unreported variants of light chain variable genes. We selected 14 variants for validation and successfully validated 11 by Sanger sequencing. Clustering of light chain 5′UTR, L-PART1, and L-PART2 revealed partial intron retention in 11 kappa and 9 lambda V alleles. Our results provide insight into germline variation in human light chain immunoglobulin loci.

MYOTONIC DYSTROPHY: EP.238 Masseter muscle volume as a disease marker in adult-onset myotonic dystrophy type 1

Myotonic dystrophy type 1 (DM1) is an autosomal dominant genetic condition characterized by multisystem involvement. Given the recent commencement of clinical trials in DM1, reliable outcome measures assessing different disease manifestations need to be investigated and validated, while keeping the total number of assessments to a minimum. In this study we used magnetic resonance (MR) images of the head of DM1 patients from a previous study to investigate the clinical correlations of masseter muscle volume and evaluate its potential use as a marker of muscle involvement. Data from 39 DM1 patients and 20 age-matched control participants who had previously undergone MR imaging of the head, completed a range of clinical outcome measures and had CTG repeat measured by small-pool PCR was used. Single rater performed manual segmentation of each masseter muscle in all participants to estimate its volume. The masseter muscle was atrophied in DM1 patients when compared to controls (p<0.001). Significant correlations were discovered between masseter volume and genetic determinants of disease severity, including estimated progenitor allele length (p=0.001) and modal allele length (p=0.003), as well as the disease duration (p=0.009). After correction for lean body mass, masseter volume was inversely correlated with self-reported myotonia (p=0.014), and with muscle function quantified using the muscle impairment rating scale (p=0.008). Masseter muscle atrophy is common in DM1 patients, and is easily quantified on MRI. The masseter volume correlates with genetic determinants of disease and measures of muscle involvement, suggesting these changes reflect the underlying disease process. Further studies evaluating masseter muscle through quantitative MRI methods may yield useful insights for outcome measure selection, and demonstrate that data regarding both central and peripheral disease may be gained from MRI brain in DM1 patients.

Association of the killer immunoglobulin-like receptor genes KIR2DS1 and KIR2DS4 with pediatric autoimmune hepatitis type I in Egypt

BackgroundKiller cell immunoglobulin-like receptors (KIR) are considered to be the key receptors that control the development and function of human natural killer cells which play complex mechanisms in autoimmune diseases. We aimed in this study to assess possible associations between killer cell immunoglobulin-like receptors (KIR2DS1 and 2DS4) genes and susceptibility to autoimmune hepatitis type I in Egyptian children.ResultsIn the case-control study conducted on eighty children diagnosed as autoimmune hepatitis (AIH) type I and eighty apparently healthy age and sex-matched control, we found that KIR2DS1, -2DS4, KIR2DS4-full length allele, and homozygous KIR2DS4-full/full variant were significantly associated with AIH-I, while the KIR1D allele and homozygous KIR2DS4-del/del variant were significantly observed in controls (P < 0.05 each). Absence of KIR2DS4 gene was significant among ANA positive AIH-I patients, patients on steroid therapy alone, and patients showing complete disease remission (P < 0.05 each). Higher activity and fibrosis indices were found significantly in patients lacking one or both studied genes.ConclusionsChildren carrying KIR2DS1, -2DS4 genes, KIR2DS4-full length allele, and homozygous KIR2DS4-full/full variant could be more susceptible to develop autoimmune hepatitis type I.

Rare minisatellite alleles of MUC2-MS8 influence susceptibility to rectal carcinoma.

Previously, we identified eight novel minisatellites in the MUC2, of which allelic variants in MUC2-MS6 were examined to influence susceptibility to gastric cancer. However, studies on the susceptibility to gastrointestinal cancer of other minisatellites in the MUC2 region still remain unprogressive. In this study, we investigated whether polymorphic variations in the MUC2-MS8 region are related to susceptibility to gastrointestinal cancer. We assessed the association between MUC2-MS8 and gastrointestinal cancers by a case-control study with 1229 controls, 486 gastric cancer cases, 220 colon cancer cases and 278 rectal cancer cases. To investigate whether intronic minisatellites affect gene expression, various minisatellites were inserted into the luciferase-reporter vector and their expression levels were examined. We also examined the length of MUC2-MS8 alleles in blood and cancer tissue matching samples of 107 gastric cancer patients, 125 colon cancer patients, and 85 rectal cancer patients, and investigated whether the repeat sequence affects genome instability. A statistically significant association was identified between rare MUC2-MS8 alleles and the occurrence of rectal cancer: odds ratio (OR), 6.66; 95% confidence interval (CI), 1.11-39.96; and P = 0.0165. In the younger group (age, < 55), rare alleles were significant associated with an increased risk of rectal cancer (odds ratio, 24.93 and P = 0.0001). Suppression of expression was found in the reporter vector inserted with minisatellites, and loss of heterozygosity (LOH) of the MUC2-MS8 region was confirmed in cancer tissues of gastrointestinal cancer patients (0.8-5.9%). Our results suggest that the rare alleles of MUC2-MS8 could be used to identify the risk of rectal cancer and that this repeat region is related to genomic instability.

Myotonic dystrophy type 1 (DM1) clinical subtypes and CTCF site methylation status flanking the CTG expansion are mutant allele length-dependent

Myotonic dystrophy type 1 (DM1) is a complex disease with a wide spectrum of symptoms. The exact relationship between mutant CTG repeat expansion size and clinical outcome remains unclear. DM1 congenital patients (CDM) inherit the largest expanded alleles, which are associated with abnormal and increased DNA methylation flanking the CTG repeat. However, DNA methylation at the DMPK locus remains understudied. Its relationship to DM1 clinical subtypes, expansion size and age-at-onset is not yet completely understood. Using pyrosequencing-based methylation analysis on 225 blood DNA samples from Costa Rican DM1 patients, we determined that the size of the estimated progenitor allele length (ePAL) is not only a good discriminator between CDM and non-CDM cases (with an estimated threshold at 653 CTG repeats), but also for all DM1 clinical subtypes. Secondly, increased methylation at both CTCF sites upstream and downstream of the expansion was almost exclusively present in CDM cases. Thirdly, levels of abnormal methylation were associated with clinical subtype, age and ePAL, with strong correlations between these variables. Fourthly, both ePAL and the intergenerational expansion size were significantly associated with methylation status. Finally, methylation status was associated with ePAL and maternal inheritance, with almost exclusively maternal transmission of CDM. In conclusion, increased DNA methylation at the CTCF sites flanking the DM1 expansion could be linked to ePAL, and both increased methylation and the ePAL could be considered biomarkers for the CDM phenotype.

TOMM40\u2018523\u2019 poly-T repeat length is a determinant of longitudinal cognitive decline in Parkinson\u2019s disease

The translocase of outer mitochondrial membrane 40 (TOMM40) ‘523’ polymorphism has previously been associated with age of Alzheimer’s disease onset and cognitive functioning in non-pathological ageing, but has not been explored as a candidate risk marker for cognitive decline in Parkinson’s disease (PD). Therefore, this longitudinal study investigated the role of the ‘523’ variant in cognitive decline in a patient cohort from the Parkinson’s Progression Markers Initiative. As such, a group of 368 people with PD were assessed annually for cognitive performance using multiple neuropsychological protocols, and were genotyped for the TOMM40 ‘523’ variant using whole-genome sequencing data. Covariate-adjusted generalised linear mixed models were utilised to examine the relationship between TOMM40 ‘523’ allele lengths and cognitive scores, while taking into account the APOE ε genotype. Cognitive scores declined over the 5-year study period and were lower in males than in females. When accounting for APOE ε4, the TOMM40 ‘523’ variant was not robustly associated with overall cognitive performance. However, in APOE ε3/ε3 carriers, who accounted for ~60% of the whole cohort, carriage of shorter ‘523’ alleles was associated with more severe cognitive decline in both sexes, while carriage of the longer alleles in females were associated with better preservation of global cognition and a number of cognitive sub-domains, and with a delay in progression to dementia. The findings indicate that when taken in conjunction with the APOE genotype, TOMM40 ‘523’ allele length is a significant independent determinant and marker for the trajectory of cognitive decline and risk of dementia in PD.

Genotype-associated cerebellar profiles in ALS: focal cerebellar pathology and cerebro-cerebellar connectivity alterations

ObjectiveCerebellar disease burden and cerebro-cerebellar connectivity alterations are poorly characterised in amyotrophic lateral sclerosis (ALS) despite the likely contribution of cerebellar pathology to the clinical heterogeneity of the condition.MethodsA prospective...

Body Remains Left by Bird Predators as a Reliable Source for Population Genetic Studies in the Great Capricorn Beetle Cerambyx cerdo, a Veteran Oak Specialist.

Simple SummaryMolecular genetic techniques can support species conservation by providing information about processes critical to population survival. Unfortunately, obtaining biological material for DNA extraction is often associated with an adverse impact on the animals under study. In legally protected or threatened species, non-invasive sampling (i.e., sampling without injuring or disturbing an animal) is preferred as it carries no risk to the population’s survival. Here, we tested the possibility of using body remains left by bird predators for microsatellite genotyping in Cerambyx cerdo, a veteran oak specialist. We compared results obtained from such remains samples with samples of fresh beetle tarsi (i.e., invasive and destructive but non-lethal samples). We found that the sample type had no significant effect on PCR amplification efficiency; instead, it was strongly affected by allele length and individual heterozygosity. Allele frequencies were perfectly correlated for both sample types (R2 = 0.94). Although point estimates of individual inbreeding were higher in remains than fresh samples (medians 0.08 vs. 0.02, respectively), both groups were not significantly different from each other and zero. Our study demonstrated that non-invasive remains samples could provide satisfactory data for population–genetic studies. However, we highlight the problem of potentially biased inbreeding estimates, which may result from allelic dropout.Obtaining biological material for DNA extraction is often challenging in organisms of conservation interest. Non-invasive sampling (i.e., sampling without injuring or disturbing an animal) is preferred as it carries no risk to the population’s survival. Here, we tested the possibility of using the body remains left by bird predators for microsatellite genotyping in Cerambyx cerdo, a veteran oak specialist. We compared results obtained from such potentially degraded samples with samples of fresh beetle tarsi (i.e., invasive and destructive but non-lethal samples). Using 10 SSR loci, we genotyped 28 fresh, and 28 remains samples. The analysis indicated that PCR amplification efficiency was not influenced by sample type but allele length and individual heterozygosity. Allele frequencies were perfectly correlated for both sample types (R2 = 0.94). Additionally, null allele frequencies and genotyping failure rates were not significantly different from zero. Although the point estimates of individual inbreeding rates (fi) were higher in remains than fresh samples (medians 0.08 vs. 0.02, respectively), both groups were not significantly different from each other and zero. Our study demonstrated that non-invasive remains samples could provide satisfactory data for population–genetic studies. However, we highlight the problem of biased inbreeding estimates, which may result from samples affected by allelic dropout.

Mutation analysis of 28 autosomal short tandem repeats in the Chinese Han population.

Short tandem repeats (STRs) have been extensively used in forensic genetics. However, according to previous studies, the mutation rates of STRs are relatively high and are affected by many factors. Therefore, it is important to analyze STR mutations and determine the influence of underlying factors on STR mutation rates. Mutation rates of 28 autosomal STRs were determined from 8708 paternity testing cases in the Chinese Han population, and the relationships between STR mutation rates and population, sex, age, allele length and heterozygosity were investigated. A total of 279 mutations were observed at 27 loci in a total of 233,530 meiosis cases, including 273 (97.8%) one-step, 5 (1.8%) two-step and 1 (0.4%) three-step mutations. The overall average mutation rate was 1.19 × 10-3 (95% CI 1.06 × 10-3 - 1.34 × 10-3) ranging from 0 (TPOX) to 2.79 × 10-3 (D13S325). Mutation rate comparisons revealed statistically significant differences at several STRs among populations. Paternal mutations occurred more frequently than maternal mutations, at a ratio of 6.04:1, and the mutation rate tended to increase with paternal age. Moreover, our study revealed a bias towards contraction mutations for long alleles and expansion mutations for short alleles. No obvious bias was observed in the overall mutation direction. In addition, STR loci with higher expected heterozygosity (Hexp) tended to have higher mutation rates. This work revealed the relationships between STR mutation rates and several influencing factors, providing useful data and information for further research on STR mutations in forensic genetics.