Linkage Peak Research Articles

Whole Genome Linkage and Association Analyses Identify DLG Associated Protein-1 as a Novel Positional and Biological Candidate Gene for Muscle Strength: The Long Life Family Study.

Grip strength is a robust indicator of overall health, is moderately heritable, and predicts longevity in older adults. Using genome-wide linkage analysis, we identified a novel locus on chromosome 18p (mega-basepair region: 3.4-4.0) linked to grip strength in 3755 individuals from 582 families aged 64 ± 12 years (range 30-110 years; 55% women). There were 26 families that contributed to the linkage peak (cumulative logarithm of the odds [LOD] score = 10.94), with 6 families (119 individuals) accounting for most of the linkage signal (LOD = 6.4). In these 6 families, using whole genome sequencing data, we performed association analyses between the 7312 single nucleotide (SNVs) and insertion deletion (INDELs) variants in the linkage region and grip strength. Models were adjusted for age, age2, sex, height, field center, and population substructure. We found significant associations between genetic variants (8 SNVs and 4 INDELs, p < 5×10-5) in the Disks Large-associated Protein 1 (DLGAP1) gene and grip strength. Haplotypes constructed using these variants explained up to 98.1% of the LOD score. Finally, RNAseq data showed that these variants were significantly associated with the expression of nearby Myosin Light Chain 12A (MYL12A), Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1), Erythrocyte Membrane Protein Band 4.1 Like 3 (EPB41L3) genes (p < .0004). The DLGAP1 gene plays an important role in the postsynaptic density of neurons; thus, it is both a novel positional and biological candidate gene for follow-up studies aimed at uncovering genetic determinants of muscle strength.

A Novel Gene ARHGAP44 for Longitudinal Changes in Glycated Hemoglobin (HbA1c) in Subjects without Type 2 Diabetes: Evidence from the Long Life Family Study (LLFS) and the Framingham Offspring Study (FOS).

Glycated hemoglobin (HbA1c) indicates average glucose levels over three months and is associated with insulin resistance and type 2 diabetes (T2D). Longitudinal changes in HbA1c (ΔHbA1c) are also associated with aging processes, cognitive performance, and mortality. We analyzed ΔHbA1c in 1,886 non-diabetic Europeans from the Long Life Family Study to uncover gene variants influencing ΔHbA1c. Using growth curve modeling adjusted for multiple covariates, we derived ΔHbA1c and conducted linkage-guided sequence analysis. Our genome-wide linkage scan identified a significant locus on 17p12. In-depth analysis of this locus revealed a variant rs56340929 (explaining 27% of the linkage peak) in the ARHGAP44 gene that was significantly associated with ΔHbA1c. RNA transcription of ARHGAP44 was associated with ΔHbA1c. The Framingham Offspring Study data further supported these findings on the gene level. Together, we found a novel gene ARHGAP44 for ΔHbA1c in family members without T2D. Follow-up studies using longitudinal omics data in large independent cohorts are warranted.

Abstract 137: Identification Of A Noncoding Genetic Variant In The Tissue Factor Locus That Reverses Lethal Thrombosis In Mice

Background: Thrombosis is initiated by tissue factor (TF, gene name F3 ) binding to coagulationFVII, with tissue factor pathway inhibitor (TFPI) inhibiting this complex. Alterations in TF orTFPI expression significantly affect thrombosis. Reducing TFPI expression by 50% ( Tfpi +/-) inmice results in a perinatal lethal phenotype on the Factor V Leiden homozygous( F5 L/L )prothrombotic background. We used the F5 L/L Tfpi +/- lethal phenotype to conduct a dominantsensitized whole genome ENU mutagenesis screen to suppress the F5 L/L Tfpi +/- lethality. Weidentified a Modifier of Factor 5 Leiden 6 (MF5L6) line with 72% penetrance and 85 F5 L/L Tfpi +/- offspring. A significant linkage peak (LOD=4.35),explaining half the suppressing effect andcontaining F3 (Chromosome 3) was identified. Goals/Hypothesis: To identify the genomic variant controlling F3 expression in the MF5L6 line. Methods: To quantify F3 expression in the surviving mice from MF5L6, quantitative PCR onliver, lung, and heart tissues from MF5L6 was performed. We used Sanger DNA and highthroughput sequencing to identify candidate TF regulatory variants in the F3 locus. Theprothrombin time assay was used to test the effects of reduced TF expression on in vitro bloodcoagulation. Results: Two distinct expression profiles in the lung and liver of the MF5L6 mice wereobserved, those that had a 50% reduction in F3 mRNA and those that did not. Heart tissuesexhibited one expression profile, suggesting that the variant regulates F3 expressiontissue-specifically. Sanger sequencing of the F3 coding region revealed no coding mutations inMF5L6 mice. Whole genome sequencing identified two novel candidate variants (in unknownF3 regulatory elements) in the 200 kilobase upstream region of F3 . The 50% reduction in F3 resulted in significant changes in coagulation by the prothrombin assay (n=18,p&lt;0.0009). Conclusion: We identified novel candidate variants for regulating F3 gene expression and aredetermining their mechanism of action. Investigation of these variants will provide new insightsinto the regulation of F3 and enable us to identify the variant(s) responsible for the remainder ofthe thrombosis suppressing effect in MF5L6. Our findings provide new insights into the geneticregulation of thrombosis.

Novel breast cancer susceptibility loci under linkage peaks identified in African ancestry consortia.

Expansion of genome-wide association studies across population groups is needed to improve our understanding of shared and unique genetic contributions to breast cancer. We performed association and replication studies guided by a priori linkage findings from African ancestry (AA) relative pairs. We performed fixed-effect inverse-variance weighted meta-analysis under three significant AA breast cancer linkage peaks (3q26-27, 12q22-23, and 16q21-22) in 9241 AA cases and 10 193 AA controls. We examined associations with overall breast cancer as well as estrogen receptor (ER)-positive and negative subtypes (193,132 SNPs). We replicated associations in the African-ancestry Breast Cancer Genetic Consortium (AABCG). In AA women, we identified two associations on chr12q for overall breast cancer (rs1420647, OR = 1.15, p = 2.50×10-6; rs12322371, OR = 1.14, p = 3.15×10-6), and one for ER-negative breast cancer (rs77006600, OR = 1.67, p = 3.51×10-6). On chr3, we identified two associations with ER-negative disease (rs184090918, OR = 3.70, p = 1.23×10-5; rs76959804, OR = 3.57, p = 1.77×10-5) and on chr16q we identified an association with ER-negative disease (rs34147411, OR = 1.62, p = 8.82×10-6). In the replication study, the chr3 associations were significant and effect sizes were larger (rs184090918, OR: 6.66, 95% CI: 1.43, 31.01; rs76959804, OR: 5.24, 95% CI: 1.70, 16.16). The two chr3 SNPs are upstream to open chromatin ENSR00000710716, a regulatory feature that is actively regulated in mammary tissues, providing evidence that variants in this chr3 region may have a regulatory role in our target organ. Our study provides support for breast cancer variant discovery using prioritization based on linkage evidence.

NOVEL GENE VARIANTS ASSOCIATED WITH HBA1C CHANGES OVER TIME AMONG NONDIABETIC SUBJECTS IN THE LONG LIFE FAMILY STUDY

Abstract Longitudinal changes in HbA1c (ΔHbA1c) are associated with insulin resistance, aging, cognition, and mortality. To identify novel gene variants underlying ΔHbA1c, we conducted linkage-guided sequence analysis on 17p12 (LODs=3.59) in the Long Life Family Study, a study with familial clustering of exceptional longevity in the US and Denmark. Subjects with clinical diagnosis of diabetes or diabetes treatment and undiagnosed diabetes cases whose fasting glucose ≥ 126 mg/dl or HbA1c ≥ 6.5% were excluded. ΔHbA1c, collected from two exams 7 years apart, was derived using growth curve modeling, adjusting for age, sex, BMI, smoking, field centers and PCs, and was blom-transformed to approximate normality. We identified a significant variant under the linkage peak (ARHGAP44 rs56340929, p=1.77E-06, MAF=6%, accounting for linkage=26.5%). Taking advantage of our currently available RNAseq data, we found a significant association between quantification of ARHGAP44 RNA transcript and adjusted ΔHbA1c using 16 linkage enriched families (n=176, β = -0.24, SE=0.09, p=0.01). We also assessed currently available lipidomics data (188 metabolites, 13 compound classes) and found phosphatidylcholine (p=0.025) and lysophosphatidylcholine (p=0.02) were marginally associated with adjusted ΔHbA1c. ARHGAP44 is reportedly associated with glycemic traits and is mainly expressed in the brain. Further complete omics-data analyses in the LLFS and a replication study using the Framingham Offspring Study are underway.

LINKAGE ANALYSIS OF PERCEIVED PHYSICAL FATIGABILITY IN THE LONG LIFE FAMILY STUDY

Abstract Fatigability, whole-body fatigue anchored to specific tasks, is a highly prevalent characteristic in older adults, but the biological mechanisms underlying perceived physical fatigability are unclear. Genetic studies may identify potential biological pathways contributing to physical fatigability. The family study design of the LLFS provides a unique opportunity to explore variants associated with fatigability using whole-genome linkage analysis. Whole genome sequencing (WGS) was available for N=2462, 496 families (age 73.6±10.5 years, 54.8% women, 99% white. Perceived physical fatigability was measured with the Pittsburgh Fatigability Scale (PFS, 0-50, lower=less severe). Prevalence of lower PFS scores (&amp;lt;15) was 57.9%. Multipoint linkage analysis employing likelihood-based variance components analyses were performed to identify families and genetic loci showing strong evidence for linkage. Based on linkage analysis results, a series of association analyses were performed in the subsets of linked families for PFS Physical scores. Association analyses were conducted using linear mixed models adjusted for age, field center, principal components and familial relatedness. For all families the LOD was 2.13 at chr17:79,549,108. The HLOD of the top 27 families (n=225) was 8.97. There were 8 single nucleotide polymorphisms (SNPs) identified under the linkage peak on chromosome 17. These variants were mapped to 8 different genes involved in regulation of transcription and metabolism, cellular proliferation, signal transduction, protein trafficking, and membrane structure; all important in maintenance of cellular health. Results suggest fatigability in older adults may have multiple molecular etiologies and identified variants may allude to molecular mechanisms to target in future interventions to promote healthy aging.

TRANSCRIPTOMIC SIGNATURES OF AGING, GENETICS, AND MORTALITY RISK: FINDINGS FROM THE LONG LIFE FAMILY STUDY

Abstract The Long Life Family Study (LLFS), funded by the National Institute on Aging, is an international collaborative study of the genetics and familial components of exceptional longevity and healthy aging. We phenotyped 4,953 individuals from 539 two-generational families (1,727 proband; 3,226 offspring) at baseline (2006-2009). A second visit (2014-2017) was conducted for 2,904 (478 proband; 2,426 offspring) participants, with a third visit ongoing. The longitudinal, comprehensive in-person visits measured domains of healthy aging, including physical performance, cognition, and blood markers. Extensive genetic analyses were performed using the baseline blood draw, including genotyping with the Illumina 2.5M Human Omni array, linkage analyses with the families, whole genome sequencing using the TopMED protocol, metabolomic assays, and trascriptomics (RNA-seq). Collectively, this symposium will present novel findings that examined differences in gene expression between those of extreme old age compared to younger participants, elucidate potential new genomic regions and variants associated with ankle brachial index, examine rare variants under linkage peaks for perceived physical fatigability, and compare mortality and cause of death between LLFS and the US population. Specifically, Ms. Li will share results on gene expression profiles in aging. Then, Ms. Ressler will share findings on the genetics of ankle brachial index with linkage and association results. Next, Ms. Gay will discuss associations under the linkage peak for perceived physical fatigability. Lastly, Ms. Yao will present mortality and patterns of death in the LLFS. As Discussant, Dr. Nalini Raghavachari from the NIA will provide insights and propose future directions for LLFS.

Functionally distinct regions of the locus Leishmania major response 15 control IgE or IFNγ level in addition to skin lesions.

Leishmaniasis, a disease caused by parasites of Leishmania spp., endangers more than 1 billion people living in endemic countries and has three clinical forms: cutaneous, mucocutaneous, and visceral. Understanding of individual differences in susceptibility to infection and heterogeneity of its pathology is largely lacking. Different mouse strains show a broad and heterogeneous range of disease manifestations such as skin lesions, splenomegaly, hepatomegaly, and increased serum levels of immunoglobulin E and several cytokines. Genome-wide mapping of these strain differences detected more than 30 quantitative trait loci (QTLs) that control the response to Leishmania major. Some control different combinations of disease manifestations, but the nature of this heterogeneity is not yet clear. In this study, we analyzed the L. major response locus Lmr15 originally mapped in the strain CcS-9 which carries 12.5% of the genome of the resistant strain STS on the genetic background of the susceptible strain BALB/c. For this analysis, we used the advanced intercross line K3FV between the strains BALB/c and STS. We confirmed the previously detected loci Lmr15, Lmr18, Lmr24, and Lmr27 and performed genetic dissection of the effects of Lmr15 on chromosome 11. We prepared the interval-specific recombinant strains 6232HS1 and 6229FUD, carrying two STS-derived segments comprising the peak linkage of Lmr15 whose lengths were 6.32 and 17.4 Mbp, respectively, and analyzed their response to L. major infection. These experiments revealed at least two linked but functionally distinct chromosomal regions controlling IFNγ response and IgE response, respectively, in addition to the control of skin lesions. Bioinformatics and expression analysis identified the potential candidate gene Top3a. This finding further clarifies the genetic organization of factors relevant to understanding the differences in the individual risk of disease.

Standing genetic variation affects phenotypic heterogeneity in an SCN5A-mutation founder population with excess sudden cardiac death

The Worm Study, ascertained from a multigeneration pedigree segregating a single amino acid deletion in SCN5A (c.4850_4852delTCT, p.(Phe1617del), rs749697698), is characterized by substantial phenotypic heterogeneity and overlap of sudden cardiac death, long-QT syndrome, cardiac conduction disease, Brugada syndrome, and isorhythmic atrioventricular dissociation. Linkage analysis for a synthetic trait derived from these phenotypes identified a single peak (logarithm of the odds [LOD] = 4.52) at the SCN5A/SCN10A/SCN11A locus on chromosome3. This study explored the role of additional genetic variation in the chromosome 3 locus as a source of phenotypic heterogeneity in the Worm Study population. Genotypes underlying the linkage peak (n = 70) were characterized using microarrays. Haplotypes were determined using family-aware phasing and a population-specific reference panel. Variants with minor allele frequencies >0.10 were tested for association with cardiac conduction disease and isorhythmic dissociation using LAMP and logistic regression. Only 1 haplotype carried the p.Phe1617del/rs749697698 deletion, suggesting relatively recent development (∼18 generations); this haplotype contained 5 other missense variants spanning SCN5A/SCN10A/SCN11A. Noncarrier haplotypes (n = 74) ranged in frequency from 0.5% to 5%. Although no variants were associated with cardiac conduction disease, a homozygous missense variant in SCN10A was associated with isorhythmic dissociation after correction for multiple comparisons (odds ratio 11.23; 95% confidence interval 2.76-23.39; P = 1.2 × 10-4). This variant (rs12632942) was previously associated with PR interval. Our data suggest that other variants, alongside a pathogenic mutation, are associated with phenotypic heterogeneity. Single-mutation screening may be insufficient to predict electrical heart disease in patients and family members. In the Worm Study population, segregating a pathogenic SCN5A mutation, compound variation in the SCN5A/SCN10A/SCN11A locus determines arrhythmic outcome.

A Whole-Genome Sequencing Study Implicates GRAMD1B in Multiple Sclerosis Susceptibility.

While the role of common genetic variants in multiple sclerosis (MS) has been elucidated in large genome-wide association studies, the contribution of rare variants to the disease remains unclear. Herein, a whole-genome sequencing study in four affected and four healthy relatives of a consanguineous Italian family identified a novel missense c.1801T &gt; C (p.S601P) variant in the GRAMD1B gene that is shared within MS cases and resides under a linkage peak (LOD: 2.194). Sequencing GRAMD1B in 91 familial MS cases revealed two additional rare missense and two splice-site variants, two of which (rs755488531 and rs769527838) were not found in 1000 Italian healthy controls. Functional studies demonstrated that GRAMD1B, a gene with unknown function in the central nervous system (CNS), is expressed by several cell types, including astrocytes, microglia and neurons as well as by peripheral monocytes and macrophages. Notably, GRAMD1B was downregulated in vessel-associated astrocytes of active MS lesions in autopsied brains and by inflammatory stimuli in peripheral monocytes, suggesting a possible role in the modulation of inflammatory response and disease pathophysiology.

Characterization of chromosome 5q35 risk locus in African Ancestry population.

AbstractBackgroundAs part of the Research in African American Alzheimer Disease Initiative (REAAADI) and Late‐Onset AD Family Study (LOAD), genotyping array and whole genome sequencing (WGS) data were generated for 51 families (160 affected and 318 unaffected). Multipoint linkage analyses identified a peak LOD score on chr5q35 (HLOD=3.20). Additionally, a suggestive locus flanking the 1‐LOD score was previously identified in an AA GWAS study (p‐value=2.6×10‐6) (Kunkle et al, 2019). Here, we further characterize this locus and its role in AD.MethodWe performed region‐wide association analysis in an independent REAAADI dataset of ∼240 cases and ∼650 controls to fine map the signal in the locus. Additionally, we analyzed the WGS data to prioritize variants in the consensus regions based on segregation with disease among affected individuals and rarity (MAF&lt;0.01). All variants were annotated for putative function including protein changes for coding variants and evidence for regulatory activity (ENCODE, RoadMap Epigenome) and chromatin interactions (publicly available HiC and promoter capture C) for noncoding variants.ResultRegion‐wide association analysis identified two regions of rare (MAF∼0.01) variants downstream (p=3.0×10‐8) and upstream (p=3.7×10‐6) of the 1‐LOD linkage region. Segregation analysis using WGS data identified 111 rare variants (MAF&lt;0.01) segregating with disease in the AD individuals of the family with the highest LOD score contributing to the linkage peak. These include a 3’UTR and synonymous variant in INSYN2B/FAM196B as well as a promoter variant in WWC1/KIBRA. Interestingly, four other AA families contributing to the chr5 linkage signal harbor different within‐family shared variants located in INSYN2B’s promoter or in enhancer regions with evidence for interaction with INSYN2B’s promoter. WWC1, expressed in astrocytes, was previously reported in AD context, whereas novel candidate INSYN2B encodes an inhibitory synaptic factor active in oligodendrocytes and neurons.ConclusionOur initial analyses provide evidence for two candidate genes contributing to AD genetics in the AA population. Additional work for functional validation of these candidates for AD is ongoing. This AA population‐specific finding shows the importance of diversifying population‐level genetic data to better understand the genetic determinants of AD on a global scale.

Weathering resistance (UV-shielding) improvement of a polyurethane automotive clear-coating applying metal-organic framework (MOF) modified GO nano-flakes (GO-ZIF-7)

In this research, ZIF-7 particles were synthesized over graphene oxide (GO) nanosheets and characterized through various techniques. Then, the influence of the fabricated GO-ZIF-7 nano-hybrids on the weathering resistance and physical-mechanical performance of the PU coatings were investigated. The weathering resistance of PU/GO-ZIF-7, PU/GO, and control PU was examined with the aid of QUV accelerated weathering conditions via several methods such as recording gloss retention and contact angle changes, FTIR, colorimetric, FE-SEM, and AFM analysis. For the PU/GO-ZIF-7 nanocomposite coating exposed to accelerated weathering condition, the changes in carbonyl group relate peak and urethane linkage were less than the changes of these parameters for the control PU sample. The change in the color component (Δb*) decreased to 56.9% of PU/GO-ZIF-7 compared to control PU (70.9%). The change of root mean square (RMS) roughness value of PU/GO-ZIF-7 was less than that of control PU (from 9.44 to 8.04 nm vs. from 14.89 to 8.02 nm). As a result, after a long weathering exposure (UV-A), the fewer changes in aesthetic properties, chemical structure, and topology of the PU/GO-ZIF-7 coating led to less surface degradation and better weathering stability performance. The GO-ZIF-7 nano-hybrids revealed that they are capable of improving the photo-stability of PU coatings by the mixed mechanisms of absorbing UV rays and free radical scavengers. The physical-mechanical characteristics of the nanocomposites were analyzed using dynamic mechanical thermal analysis (DMTA) and tensile tests. The addition of GO-ZIF-7 to PU led to an above 70% and 85% increase of elongation at break and toughness concerning the control PU, respectively.

Bio-based Polyurethane Derived from Carbon Dioxide and Epoxidized Soybean Oil

The synthesis of polyurethane relies on a toxic and petroleum-based isocyanate reactant. The aim of this research was to synthesize Polyurethane using environment-benign and renewable starting materials such as carbon dioxide and soybean oil. The carbonated soybean oil was first prepared from carbon dioxide (CO2) and epoxidized soybean oil (ESBO) using zinc glutarate (ZnGA) as a catalyst but the result of FTIR indicated the absence of the peak of cyclic carbonate around 1800 cm-1. Therefore, in this work, the synthesis of Polyurethane was modified from A. Lee (Lee &amp; Deng, 2015) using tetramethylammonium bromide (TBAB) as a catalyst. The as-synthesized carbonated soybean oil (CSBO) was allowed to react with two types of substances, 3-aminopropyltriethoxysilane or diethylenetriamine with the molar ratios of cyclic carbonate:NH2 of 1:1 with THF or DMF as solvents to obtain Polyurethanes (U1THF, U1DMF, U2THF, U2DMF). After 3 hours lignin solution was added to form a film. Raman spectra confirmed the catalyst removal from CSBO. FTIR spectra showed the peak around 1800 cm-1 assigned to cyclic carbonate of CSBO, and a new peak of urethane linkage around 1700 cm-1 (C=O stretching) of Polyurethanes. The conversion of epoxide to cyclic carbonate was also confirmed by 1H-NMR. Upon adding lignin into the Polyurethanes, the lignin-urethane U1THF, and U1DMF formed films whereas U2THF, and U2DMF formed viscous liquids. In terms of applications, all four formulations can be potentially applied as bioadhesives.

Whole genome sequencing identifies candidate genes for familial essential tremor and reveals biological pathways implicated in essential tremor aetiology.

SummaryBackgroundEssential tremor (ET), one of the most common neurological disorders, has a phenotypically heterogeneous presentation characterized by bilateral kinetic tremor of the arms and, in some patients, tremor involving other body regions (e.g., head, voice). Genetic studies suggest that ET is genetically heterogeneous.MethodsWe analyzed whole genome sequence data (WGS) generated on 104 multi-generational white families with European ancestry affected by ET. Genome-wide parametric linkage and association scans were analyzed using adjusted logistic regression models through the application of the Pseudomarker software. To investigate the additional contribution of rare variants in familial ET, we also performed an aggregate variant non-parametric linkage (NPL) analysis using the collapsed haplotype method implemented in CHP-NPL software.FindingsParametric linkage analysis of common variants identified several loci with significant evidence of linkage (HLOD ≥3.6). Among the gene regions within the strongest ET linkage peaks were BTC (4q13.3, HLOD=4.53), N6AMT1 (21q21.3, HLOD=4.31), PCDH9 (13q21.32, HLOD=4.21), EYA1 (8q13.3, HLOD=4.04), RBFOX1 (16p13.3, HLOD=4.02), MAPT (17q21.31, HLOD=3.99) and SCARB2 (4q21.1, HLOD=3.65). CHP-NPL analysis identified fifteen additional genes with evidence of significant linkage (LOD ≥3.8). These genes include TUBB2A, VPS33B, STEAP1B, SPINK5, ZRANB1, TBC1D3C, PDPR, NPY4R, ETS2, ZNF736, SPATA21, ARL17A, PZP, BLK and CCDC94. In one ET family contributing to the linkage peak on chromosome 16p13.3, we identified a likely pathogenic heterozygous canonical splice acceptor variant in exon 2 of RBFOX1 (ENST00000547372; c.4-2A>G), that co-segregated with the ET phenotype in the family.InterpretationLinkage and association analyses of WGS identified several novel ET candidate genes, which are implicated in four major pathways that include 1) the epidermal growth factor receptor-phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha-AKT serine/threonine kinase 1 (EGFR-PI3K-AKT) and Mitogen-activated protein Kinase 1 (ERK) pathways, 2) Reactive oxygen species (ROS) and DNA repair, 3) gamma-aminobutyric acid-ergic (GABAergic) system and 4) RNA binding and regulation of RNA processes. Our study provides evidence for a possible overlap in the genetic architecture of ET, neurological disease, cancer and aging. The genes and pathways identified can be prioritized in future genetic and functional studies.FundingNational Institutes of Health, NINDS, NS073872 (USA) and NIA AG058131(USA).

Genetic substrates of bipolar disorder risk in Latino families.

Genetic studies of bipolar disorder (BP) have been conducted in the Latin American population, to date, in several countries, including Mexico, the United States, Costa Rica, Colombia, and, to a lesser extent, Brazil. These studies focused primarily on linkage-based designs utilizing families with multiplex cases of BP. Significant BP loci were identified on Chromosomes 18, 5 and 8, and fine mapping suggested several genes of interest underlying these linkage peaks. More recently, studies in these same pedigrees yielded significant linkage loci for BP endophenotypes, including measures of activity, sleep cycles, and personality traits. Building from findings in other populations, candidate gene association analyses in Latinos from Mexican and Central American ancestry confirmed the role of several genes (including CACNA1C and ANK3) in conferring BP risk. Although GWAS, methylation, and deep sequencing studies have only begun in these populations, there is evidence that CNVs and rare SNPs both play a role in BP risk of these populations. Large segments of the Latino populations in the Americas remain largely unstudied regarding BP genetics, but evidence to date has shown that this type of research can be successfully conducted in these populations and that the genetic underpinnings of BP in these cohorts share at least some characteristics with risk genes identified in European and other populations.

Targeted Genome Sequencing Identifies Multiple Rare Variants inCaveolin-1 Associated with Obstructive Sleep Apnea.

Rationale: Obstructive sleep apnea (OSA) is a common disorder associated with increased risk for cardiovascular disease, diabetes, and premature mortality. There is strong clinical and epidemiologic evidence supporting the importance of genetic factors influencing OSA but limited data implicating specific genes. Objectives: To search for rare variants contributing to OSA severity. Methods: Leveraging high-depth genomic sequencing data from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and imputed genotype data from multiple population-based studies, we performed linkage analysis in the CFS (Cleveland Family Study), followed by multistage gene-based association analyses in independent cohorts for apnea-hypopnea index (AHI) in a total of 7,708 individuals of European ancestry. Measurements and Main Results: Linkage analysis in the CFS identified a suggestive linkage peak on chromosome 7q31 (LOD = 2.31). Gene-based analysis identified 21 noncoding rare variants in CAV1 (Caveolin-1) associated with lower AHI after accounting for multiple comparisons (P = 7.4 × 10-8). These noncoding variants together significantly contributed to the linkage evidence (P < 10-3). Follow-up analysis revealed significant associations between these variants and increased CAV1 expression, and increased CAV1 expression in peripheral monocytes was associated with lower AHI (P = 0.024) and higher minimum overnight oxygen saturation (P = 0.007). Conclusions: Rare variants in CAV1, a membrane-scaffolding protein essential in multiple cellular and metabolic functions, are associated with higher CAV1 gene expression and lower OSA severity, suggesting a novel target for modulating OSA severity.

Abstract 2497: Inherited copy number variants that increase risk of developing pediatric germ cell tumors with a particular focus on the X chromosome

Abstract Pediatric malignant germ cell tumors (GCTs) are heterogeneous but are grouped together due to the presumed common cell of origin, the primordial germ cell (PGC). Little is known about etiology; however, evidence supporting in utero origins of pediatric and adult GCT suggests that disruptions in normal germ cell development are likely to be highly relevant. Germline copy number variants (CNVs) are a plausible source of inherited genetic variation and have not been thoroughly evaluated to date. CNVs on the X chromosome are of particular interest because individuals with both Klinefelter syndrome (47, XXY) and Turner syndrome (45, X) are at increased risk of pediatric GCT, suggesting that alterations in X chromosome dosage contribute to etiology. A family study of adult testicular cancer where at least one member had bilateral cancer identified a significant linkage peak at Xq27 (hLOD=4.7). In addition, somatic copy number gains of chromosome X are frequently seen in adult testicular germ cell tumors. Given these findings in adult GCT, similar aberrations may also be relevant risk factors for the pediatric group. Pediatric GCT samples were obtained from a Children’s Oncology Group study and state biobank programs in Michigan and California. Genotyping array data were generated using the Illumina HumanCoreExome Beadchip (Illumina, San Diego). CNV calls were made for 2,002 GCT cases and 1,402 controls with high quality intensity data using Genvisis, which has specialized algorithms to make CNV calls on the X chromosome. Klinefelter syndrome cases (n=27) were excluded from the analyses. No study sample had classic Turner syndrome; however, one female case had a giant 51Mb deletion of Xq. Analyses were performed for females-only, males-only, and everyone together. We identified two regions that are study-wide significant on chromosome X at Xq27.1 and Xp11.2 and one nominally significant near Xq28. The most significant finding was identified in females-only and is located within a region that encodes genes within the SPANX family. Evidence suggests these genes affect germ cells; however, supporting data is reported in spermatozoa rather than oocytes. The events in our study were large (240kb), had similar breakpoints, and appear to be flanked by repetitive DNA that might lead to recurrent events at the same region. The variant was present in the control samples within gnomAD at a low allele frequency (0.18%). In our study, both deletions and duplications were noted: 11 female cases (1 or 2 expected based on gnomAD allele frequencies) and 0 female controls (0-1 expected). The finding was not replicated in males (6 male cases and 5 male controls harbored similar CNVs). We are in the process of validating these in silico and potentially via quantitative PCR. Findings may shed light on disruptions in normal development that may increase risk of GCT. Citation Format: Shannon S. Cigan, John J. Meredith, John Zaharick, Erica Langer, Anthony J. Hooten, John A. Lane, Nathan Pankratz, Jenny N. Poynter. Inherited copy number variants that increase risk of developing pediatric germ cell tumors with a particular focus on the X chromosome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2497.

Synthesis and characterization of SiO2-NiO xerogel nanocomposite prepared by sol–gel method for catalytic reduction of p-nitrophenol

This manuscript describes the preparation and characterization of silica-nickel oxide (SiO2-NiO) xerogel nanocomposite and its catalytic application in the hydrogenation of p-nitrophenol. Hydrochloric acid and ammonium hydroxide were used as the acid and base catalyst, respectively during the synthesis of SiO2-NiO. The Fourier Transformation Infra-Red spectroscopic results supported the formation of the silica xerogel skeleton structure with corresponding characteristic peaks of siloxane linkage. The surface of SiO2-NiO xerogel nanocomposite was observed to be porous along with some irregular cracks. The X-Ray diffraction analysis showed that the SiO2-NiO xerogel nanocomposite was amorphous in nature. The synthesized xerogel nanocomposite was employed as a catalyst for the hydrogenation of p-nitrophenol with sodium borohydride in water. The rate of hydrogenation of p-nitrophenol was observed to be increased with the increased amount of catalyst as well as the temperature. The maximum reduction rate of p-nitrophenol was found as high as 0.26 min-1.

Identification of Chromosomal Regions Linked to Autism-Spectrum Disorders: A Meta-Analysis of Genome-Wide Linkage Scans.

Background: Autism spectrum disorder (ASD) is a clinically and genetically heterogeneous group of pervasive neurodevelopmental disorders with a strong hereditary component. Although, genome-wide linkage scans (GWLS) and association studies (GWAS) have previously identified hundreds of ASD risk gene loci, the results remain inconclusive. Method: We performed a heterogeneity-based genome search meta-analysis (HEGESMA) of 15 genome scans of autism and ASD. Results: For strictly defined autism, data were analyzed across six separate genome scans. Region 7q22-q34 reached statistical significance in both weighted and unweighted analyses, with evidence of significantly low between-scan heterogeneity. For ASDs (data from 12 separate scans), chromosomal regions 5p15.33-5p15.1 and 15q22.32-15q26.1 reached significance in both weighted and unweighted analyses but did not reach significance for either low or high heterogeneity. Region 1q23.2-1q31.1 was significant in unweighted analyses with low between-scan heterogeneity. Finally, region 8p21.1-8q13.2 reached significant linkage peak in all our meta-analyses. When we combined all available genome scans (15), the same results were produced. Conclusions: This meta-analysis suggests that these regions should be further investigated for autism susceptibility genes, with the caveat that autism spectrum disorders have different linkage signals across genome scans, possibly because of the high genetic heterogeneity of the disease.

Novel Positional and Biological Candidate Gene for Grip Strength in Older Adults: The Long Life Family Study

Grip strength is a robust indicator of overall health, is moderately heritable and predicts longevity in older adults. Using genome-wide linkage analysis, we identified a novel locus on chromosome 18p linked to grip strength in 4534 individuals from 582 families (age 70.0 ± 15.8, range 24–110 years; 54% women). DNA sequencing was completed to identify single nucleotide variants (SNVs) in the 3.44 – 4.04 mega-basepair region on chromosome 18p. Using the sequencing data, we performed association analyses between the 7312 SNVs in the region and grip strength in families exhibiting evidence for linkage. Models were adjusted for age, age2, sex, height, field center and population substructure. There were 23 families (263 individuals) that contributed to the linkage peak (cumulative logarithm of the odds [LOD] score = 12.4). Six families (112 individuals) accounted for most of the linkage signal (LOD = 6.4). In these 6 families, we found highly significant associations between SNVs in the Disks Large-associated Protein 1 (DLGAP1) gene and grip strength (lead SNV: β= -0.75kg ± 0.15, p-value= 4.3*10-6). Correcting for the top SNV in DLGAP1 reduces the LOD by 72% in these families. Further, the effect allele frequency is much higher in these 6 families (39.7%) compared with both the NHLBI’s Trans-OMICs for Precision Medicine (23.5%) and 1000Genomes (28.0%) references panels. The DLGAP1 gene plays an important role in post-synaptic density of neurons; thus, it is a novel positional and biological candidate gene for follow-up studies aimed at uncovering genetic determinants of muscle strength.