Rare Single Nucleotide Polymorphisms Research Articles

Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates

Mitochondrial DNA (mtDNA) encodes the proteins of the electron transfer chain to produce adenosine triphosphate through oxidative phosphorylation, and is essential to sustain life. mtDNA is unique from the nuclear genome in so much as it is solely maternally inherited (non-mendelian patterning), and shows a relatively high rate of mutation due to the absence of error checking capacity. While it is generally assumed that most new mutations accumulate through the process of heteroplasmy, it is unknown whether mutations initiated in the mother are inherited, occur in utero, or occur and accumulate early in life. The purpose of this study is to examine the maternally heritable and de novo mutation rate in the fetal mtDNA through high-fidelity sequencing from a large population-based cohort. Samples were obtained from 90 matched maternal (blood) and fetal (placental) pairs. In addition, a smaller cohort (n= 5) of maternal (blood), fetal (placental), and neonatal (cord blood) trios were subjected to DNA extraction and shotgun sequencing. The whole genome was sequenced on the Illumina HiSeq platform (Illumina Inc., San Diego, CA), and haplogroups and mtDNA variants were identified through mapping to reference mitochondrial genomes (NC_012920). We observed 665 single nucleotide polymorphisms and 82 insertions-deletions variants identified in the cohort at large. We achieved high sequencing depth of the mtDNA to an average depth of 65X (range, 20-171X) coverage. The proportions of haplogroups identified in the cohort are consistent with the patient's self-identified ethnicity (>90% Hispanic), and all maternal-fetal pairs mapped to the identical haplogroup. Only variants from samples with average depth >20X and allele frequency >1% were included for further analysis. While the majority of the maternal-fetal pairs (>90%) demonstrated identical variants at the single nucleotide level, we observed rare mitochondrial single nucleotide polymorphism discordance between maternal and fetal mitochondrial genomes. In this first in-depth sequencing analysis of mtDNA from maternal-fetal pairs at the time of birth, a low rate of de novo mutations appears in the fetal mitochondrial genome. This implies that these mutations likely arise from the maternal heteroplasmic pool (eg, in the oocyte), and accumulate later in the offspring's life. These findings have key implications for both the occurrence and screening for mitochondrial disorders.

A pharmacogenetic candidate gene study of tenofovir-associated Fanconi syndrome.

Tenofovir disoproxil fumarate (TDF) is a widely used antiretroviral agent with favorable efficacy, safety, and tolerability profiles. However, renal adverse events, including the rare Fanconi syndrome (FS), may occur in a small subset of patients treated for HIV infections. The aim of this study was to identify genetic variants that may be associated with TDF-associated FS (TDF-FS). DNA samples collected from 19 cases with TDF-FS and 36 matched controls were sequenced, and genetic association studies were conducted on eight candidate genes: ATP-binding cassette (ABC) transporters ABCC2 (MRP2) and ABCC4 (MRP4), solute carrier family members SLC22A6 (OAT1) and SLC22A8 (OAT3), adenylate kinases 2 (AK2) and 4 (AK4), chloride transporter CIC-5 CLCN5, and Lowe syndrome protein OCRL. The functional effects of a single nucleotide polymorphism (SNP) predicted to alter the transport of tenofovir were then investigated in cells expressing an identified variant of ABCC4. The case group showed a trend toward a higher proportion of rare alleles. Six SNPs in ABCC2 (three SNPs), ABCC4 (one SNP), and OCRL (two SNPs) were associated with TDF-FS case status; however, this association did not remain significant after correction for multiple testing. Six SNPs, present in OCRL (four SNPs) and ABCC2 (two SNPs), were significantly associated with increased serum creatinine levels in the cases, and this association remained significant after multiple test correction (P < 2 × 10). One synonymous SNP in ABCC2 (rs8187707, P = 2.10 × 10, β = -73.3 ml/min/1.73 m(2)) was also significantly associated with the decreased estimated glomerular filtration rate of creatinine among cases. However, these results were driven by rare SNPs present in a small number of severely affected cases. Finally, a previously uncharacterized, nonsynonymous SNP, rs11568694, that was predicted to alter MRP4 function had no significant effect on tenofovir cellular accumulation in vitro. Although no single predictive genetic marker for the development of TDF-FS was identified, the findings from our study suggest that rare variants in multiple genes involved in the renal handling of tenofovir, and/or renal cell homeostasis, may be associated with increased susceptibility to TDF-FS.

Inference of Distant Genetic Relations in Humans Using “1000 Genomes”

Nucleotide sequence differences on the whole-genome scale have been computed for 1,092 people from 14 populations publicly available by the 1000 Genomes Project. Total number of differences in genetic variants between 96,464 human pairs has been calculated. The distributions of these differences for individuals within European, Asian, or African origin were characterized by narrow unimodal peaks with mean values of 3.8, 3.5, and 5.1 million, respectively, and standard deviations of 0.1–0.03 million. The total numbers of genomic differences between pairs of all known relatives were found to be significantly lower than their respective population means and in reverse proportion to the distance of their consanguinity. By counting the total number of genomic differences it is possible to infer familial relations for people that share down to 6% of common loci identical-by-descent. Detection of familial relations can be radically improved when only very rare genetic variants are taken into account. Counting of total number of shared very rare single nucleotide polymorphisms (SNPs) from whole-genome sequences allows establishing distant familial relations for persons with eighth and ninth degrees of relationship. Using this analysis we predicted 271 distant familial pairwise relations among 1,092 individuals that have not been declared by 1000 Genomes Project. Particularly, among 89 British and 97 Chinese individuals we found three British–Chinese pairs with distant genetic relationships. Individuals from these pairs share identical-by-descent DNA fragments that represent 0.001%, 0.004%, and 0.01% of their genomes. With affordable whole-genome sequencing techniques, very rare SNPs should become important genetic markers for familial relationships and population stratification.

Genetic associations of nonsynonymous exonic variants with psychophysiological endophenotypes.

We mapped ∼85,000 rare nonsynonymous exonic single nucleotide polymorphisms (SNPs) to 17 psychophysiological endophenotypes in 4,905 individuals, including antisaccade eye movements, resting EEG, P300 amplitude, electrodermal activity, affect-modulated startle eye blink. Nonsynonymous SNPs are predicted to directly change or disrupt proteins encoded by genes and are expected to have significant biological consequences. Most such variants are rare, and new technologies can efficiently assay them on a large scale. We assayed 247,870 mostly rare SNPs on an Illumina exome array. Approximately 85,000 of the SNPs were polymorphic, rare (MAF < .05), and nonsynonymous. Single variant association tests identified a SNP in the PARD3 gene associated with theta resting EEG power. The sequence kernel association test, a gene-based test, identified a gene PNPLA7 associated with pleasant difference startle, the difference in startle magnitude between pleasant and neutral images. No other single nonsynonymous variant, or gene-based group of variants, was strongly associated with any endophenotype.

Logistic Principal Component Analysis for Rare Variants in Gene-Environment Interaction Analysis.

The characteristics of low minor allele frequency (MAF) and weak individual effects make genome-wide association studies (GWAS) for rare variant single nucleotide polymorphisms (SNPs) more difficult when using conventional statistical methods. By aggregating the rare variant effects belonging to the same gene, collapsing is the most common way to enhance the detection of rare variant effects for association analyses with a given trait. In this paper, we propose a novel framework of MAF-based logistic principal component analysis (MLPCA) to derive aggregated statistics by explicitly modeling the correlation between rare variant SNP data, which is categorical. The derived aggregated statistics by MLPCA can then be tested as a surrogate variable in regression models to detect the gene-environment interaction from rare variants. In addition, MLPCA searches for the optimal linear combination from the best subset of rare variants according to MAF that has the maximum association with the given trait. We compared the power of our MLPCA-based methods with four existing collapsing methods in gene-environment interaction association analysis using both our simulation data set and Genetic Analysis Workshop 17 (GAW17) data. Our experimental results have demonstrated that MLPCA on two forms of genotype data representations achieves higher statistical power than those existing methods and can be further improved by introducing the appropriate sparsity penalty. The performance improvement by our MLPCA-based methods result from the derived aggregated statistics by explicitly modeling categorical SNP data and searching for the maximum associated subset of SNPs for collapsing, which helps better capture the combined effect from individual rare variants and the interaction with environmental factors.

Illumina human exome genotyping array clustering and quality control.

With the rise of high-throughput sequencing technology, traditional genotyping arrays are gradually being replaced by sequencing technology. Against this trend, Illumina has introduced an exome genotyping array that provides an alternative approach to sequencing, especially suited to large-scale genome-wide association studies (GWASs). The exome genotyping array targets the exome plus rare single-nucleotide polymorphisms (SNPs), a feature that makes it substantially more challenging to process than previous genotyping arrays that targeted common SNPs. Researchers have struggled to generate a reliable protocol for processing exome genotyping array data. The Vanderbilt Epidemiology Center, in cooperation with Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD), has developed a thorough exome chip-processing protocol. The protocol was developed during the processing of several large exome genotyping array-based studies, which included over 60,000 participants combined. The protocol described herein contains detailed clustering techniques and robust quality control procedures, and it can benefit future exome genotyping array-based GWASs.

A rare 8q24 single nucleotide polymorphism (SNP) predisposes North American men to prostate cancer and possibly more aggressive disease.

To assess the frequency of a novel prostate cancer-associated single nucleotide polymorphism (SNP), rs188140481, in a North American population and to evaluate the clinical significance of this variant including annotated prostatectomy pathology. We examined the frequency of the minor allele at rs188140481 in 4299 North American men including 1979 men with prostate cancer and 2320 healthy volunteers. We compared the clinicopathological features of prostate cancer between carriers and non-carriers of the SNP. The rs188140481[A] SNP was present in 1.6% of the cohort; it was significantly more likely to be carried by men with prostate cancer than healthy controls (odds ratio 3.14; 95% confidence interval [CI] 1.85-5.35). After adjusting for age and PSA levels, carriers were found to be 6.73-fold (95% CI 1.69-26.76) more likely to develop prostate cancer than non-carriers. Age at diagnosis, frequency of a positive family history of prostate cancer, and biochemical recurrence rates were similar between SNP carriers and non-carriers. Patients with the SNP had a proportionately higher frequency of stage ≥T2c disease (29.5% vs 20.1%; P = 0.13), Gleason ≥8 tumours (13.3% vs 6.5%; P = 0.10), and extracapsular extension (28.9% vs 18.8%; P = 0.12) compared with non-carriers. rs188140481[A] is a rare SNP that confers greater risk of prostate cancer compared with SNPs identified by genome-wide association studies. Because of its low frequency, larger studies are needed to validate the prognostic significance of this locus, and associations with adverse pathology.

495P - Contribution of Rare Germline Copy Number Variants and Single Nucleotide Polymorphisms to Familial Colorectal Cancer

ABSTRACT Aim: Lynch Syndrome (LS) is the most common hereditary disease associated with colorectal carcinomas (CRC). Approximately 50% of cases presented mutations in mismatch repair (MMR) genes. Therefore, the molecular etiology of half of patients is still largely unknown, suggesting that other genetic or epigenetic hereditary factors might be associated with the cancer predisposition. Methods: Germline copy number variations (CNVs) were screened in 58 LS patients negative for pathogenic mutations in MMR genes, using a CGH 4x180K platform (Agilent Technologies). Genomic data were analyzed with Genomic Workbench software. A CNV data of 100 healthy Brazilian women analyzed with the same platform and parameters were used as a reference group (Krepischi et al., 2012; Breast Cancer Res 14:R24). The results were compared with the Database of Genomic Variants (DGV-hg18). The CNVs were classified as rare if detected in Results: A reduced number of CNVs in cases (263; 4.5 ± 3.6 CNVs/individual) were found in comparison with the Brazilian reference dataset (706; 7.1 ± 3.2 CNVs/individual) (Mann-Whitney Test, p Conclusions: These results suggested that patients with a proficient MMR profile, rare CNVs and SNPs might contribute to the risk of CRC development in Lynch syndrome patients. Disclosure: All authors have declared no conflicts of interest.

An intronic PICALM polymorphism, rs588076, is associated with allelic expression of a PICALM isoform.

BackgroundAlthough genome wide studies have associated single nucleotide polymorphisms (SNP)s near PICALM with Alzheimer’s disease (AD), the mechanism underlying this association is unclear. PICALM is involved in clathrin-mediated endocytosis and modulates Aß clearance in vitro. Comparing allelic expression provides the means to detect cis-acting regulatory polymorphisms. Thus, we evaluated whether PICALM showed allele expression imbalance (AEI) and whether this imbalance was associated with the AD-associated polymorphism, rs3851179.ResultsWe measured PICALM allelic expression in 42 human brain samples by using next-generation sequencing. Overall, PICALM demonstrated equal allelic expression with no detectable influence by rs3851179. A single sample demonstrated robust global PICALM allelic expression imbalance (AEI), i.e., each of the measured isoforms showed AEI. Moreover, the PICALM isoform lacking exons 18 and 19 (D18-19 PICALM) showed significant AEI in a subset of individuals. Sequencing these individuals and subsequent genotyping revealed that rs588076, located in PICALM intron 17, was robustly associated with this imbalance in D18-19 PICALM allelic expression (p = 9.54 x 10-5). This polymorphism has been associated previously with systolic blood pressure response to calcium channel blocking agents. To evaluate whether this polymorphism was associated with AD, we genotyped 3269 individuals and found that rs588076 was modestly associated with AD. However, when both the primary AD SNP rs3851179 was added to the logistic regression model, only rs3851179 was significantly associated with AD.ConclusionsPICALM expression shows no evidence of AEI associated with rs3851179. Robust global AEI was detected in one sample, suggesting the existence of a rare SNP that strongly modulates PICALM expression. AEI was detected for the D18-19 PICALM isoform, and rs588076 was associated with this AEI pattern. Conditional on rs3851179, rs588076 was not associated with AD risk, suggesting that D18-19 PICALM is not critical in AD. In summary, this analysis of PICALM allelic expression provides novel insights into the genetics of PICALM expression and AD risk.

Mutation screening of HOXA7 and HOXA9 genes in Chinese women with Müllerian duct abnormalities

HOXA genes in groups 7–13 have been proven to play a role in determining positional identity along the genitalia axis. The aim of the present study was to explore the relationship between HOXA7 and HOXA9 mutations and Müllerian duct abnormalities (MDA). One hundred and ninety-two Chinese patients with MDA abnormalities and 192 healthy controls were recruited. All coding regions of HOXA7 and HOXA9 were amplified and sequenced directly. Rs2301721 and rs2301720 in HOXA7, rs35355140 and rs7810502 in HOXA9 were identified in patients with MDA and controls. One rare single nucleotide polymorphism rs189587233 in 3′ UTR of HOXA9 gene was detected in one patient with didelphic uterus and absent in the 192 controls. This polymorphism, however, is known to exist in the normal Chinese population. Our results indicated that variants in the HOXA7 and HOXA9 genes were not common in Chinese women with Müllerian duct abnormalities.

Kernel score statistic for dependent data.

The kernel score statistic is a global covariance component test over a set of genetic markers. It provides a flexible modeling framework and does not collapse marker information. We generalize the kernel score statistic to allow for familial dependencies and to adjust for random confounder effects. With this extension, we adjust our analysis of real and simulated baseline systolic blood pressure for polygenic familial background. We find that the kernel score test gains appreciably in power through the use of sequencing compared to tag-single-nucleotide polymorphisms for very rare single nucleotide polymorphisms with <1% minor allele frequency.

Proteasome Modulator 9 Gene SNPs, Responsible for Anti‐Depressant Response, Are in Linkage With Generalized Anxiety Disorder

Proteasome modulator 9 (PSMD9) gene single nucleotide polymorphism (SNP) rs1043307/rs2514259 (E197G) is associated with significant clinical response to the anti-depressant desipramine. PSMD9 SNP rs74421874 [intervening sequence (IVS) 3 + nt460 G>A], rs3825172 (IVS3 + nt437 C>T) and rs1043307/rs2514259 (E197G A>G) are all linked to type 2 diabetes (T2D), maturity-onset-diabetes-of the young 3 (MODY3), obesity and waist circumference, hypertension, hypercholesterolemia, T2D-macrovascular and T2D-microvascular disease, T2D-neuropathy, T2D-carpal tunnel syndrome, T2D-nephropathy, T2D-retinopathy, non-diabetic retinopathy and depression. PSMD9 rs149556654 rare SNP (N166S A>G) and the variant S143G A>G also contribute to T2D. PSMD9 is located in the chromosome 12q24 locus, which per se is in linkage with depression, bipolar disorder and anxiety. In the present study, we wanted to determine whether PSMD9 is linked to general anxiety disorder in Italian T2D families. Two-hundred Italian T2D families were phenotyped for generalized anxiety disorder, using the diagnostic criteria of DSM-IV. When the diagnosis was unavailable or unclear, the trait was reported as unknown. The 200 Italians families were tested for the PSMD9 T2D risk SNPs rs74421874 (IVS3 + nt460 G>A), rs3825172 (IVS3 +nt437 T>C) and for the T2D risk and anti-depressant response SNP rs1043307/rs2514259 (E197G A>G) for evidence of linkage with generalized anxiety disorder. Non-parametric linkage analysis was executed via Merlin software. One-thousand simulation tests were performed to exclude results due to random chance. In our study, the PSMD9 gene SNPs rs74421874, rs3825172, and rs1043307/rs2514259 result in linkage to generalized anxiety disorder. This is the first report describing PSMD9 gene SNPs in linkage to generalized anxiety disorder in T2D families.

Investigation of Genetic Variants, Birthweight and Hypothalamic-Pituitary-Adrenal Axis Function Suggests a Genetic Variant in the SERPINA6 Gene Is Associated with Corticosteroid Binding Globulin in the Western Australia Pregnancy Cohort (Raine) Study

BackgroundThe hypothalamic-pituitary-adrenal (HPA) axis regulates stress responses and HPA dysfunction has been associated with several chronic diseases. Low birthweight may be associated with HPA dysfunction in later life, yet human studies are inconclusive. The primary study aim was to identify genetic variants associated with HPA axis function. A secondary aim was to evaluate if these variants modify the association between birthweight and HPA axis function in adolescents.MethodsMorning fasted blood samples were collected from children of the Western Australia Pregnancy Cohort (Raine) at age 17 (n = 1077). Basal HPA axis function was assessed by total cortisol, corticosteroid binding globulin (CBG), and adrenocorticotropic hormone (ACTH). The associations between 124 tag single nucleotide polymorphisms (SNPs) within 16 HPA pathway candidate genes and each hormone were evaluated using multivariate linear regression and penalized linear regression analysis using the HyperLasso method.ResultsThe penalized regression analysis revealed one candidate gene SNP, rs11621961 in the CBG encoding gene (SERPINA6), significantly associated with total cortisol and CBG. No other candidate gene SNPs were significant after applying the penalty or adjusting for multiple comparisons; however, several SNPs approached significance. For example, rs907621 (p = 0.002) and rs3846326 (p = 0.003) in the mineralocorticoid receptor gene (NR3C2) were associated with ACTH and SERPINA6 SNPs rs941601 (p = 0.004) and rs11622665 (p = 0.008), were associated with CBG. To further investigate our findings for SERPINA6, rare and common SNPs in the gene were imputed from the 1,000 genomes data and 8 SNPs across the gene were significantly associated with CBG levels after adjustment for multiple comparisons. Birthweight was not associated with any HPA outcome, and none of the gene-birthweight interactions were significant after adjustment for multiple comparisons.ConclusionsOur study suggests that genetic variation in the SERPINA6 gene may be associated with altered CBG levels during adolescence. Replication of these findings is required.

Flow-mediated dilation, carotid wall thickness and HDL function in subjects with hyperalphalipoproteinemia

Background and aimsThe relationships between very high plasma HDLc and subclinical atherosclerosis are still a matter of debate. Methods and resultsTwenty subjects with primary hyperalphalipoproteinemia (HAL, with HDLc in the highest 10th percentile and absence of overt secondary causes of this condition), aged 30–65 years, were compared with 20 age and sex-matched controls. Lipid determination, lipoprotein particle distribution (Lipoprint®), Cholesterol Efflux Capacity (CEC), plasma adhesion molecule, analyses of CETP, SRB1 and LIPG genes and of different markers of subclinical vascular disease (ankle-brachial index, ABI; carotid intima-media thickness, cIMT; brachial-artery flow mediated dilation, FMD) were performed. Fasting HDLc levels were 40 mg/dl higher in HAL subjects while LDLc concentration was comparable to control group. CETP gene analysis in HAL subjects identified one novel rare Single Nucleotide Polymorphism (SNP, Asp131Asn), possibly damaging, while the common SNP p.Val422Ile was highly prevalent (50% vs. 27.4% in a control population). No rare mutations associated with HAL were found in SR-B1 and LIPG genes. Polyacrylamide gel electrophoresis in HAL subjects disclosed larger and more buoyant HDL particles than in controls, while LDL profile was much more similar. ABI, cIMT and arterial plaques did not differ in cases and controls and the two groups showed comparable FMD at brachial artery examination. Similarly, ABCA1 and ABCG1 HDL-mediated CEC, the most relevant for atheroprotection, did not discriminate between the groups and only ABCG1 pathway seemed somewhat related to arterial reactivity. ConclusionsHDL dimension, function and genetics seem scarcely related to subclinical atherosclerosis and vascular reactivity in middle-aged HAL subjects.

Role for Germline Mutations and a Rare Coding Single Nucleotide Polymorphism Within the KCNJ5 Potassium Channel in a Large Cohort of Sporadic Cases of Primary Aldosteronism

Primary aldosteronism (autonomous aldosterone production with suppressed renin) plays an important pathophysiological role in what has been previously labeled as essential hypertension. Besides the recently described germline mutations in the KCNJ5 potassium channel associated with familial primary aldosteronism, somatic mutations in the same channel have been identified within aldosterone-producing adenomas. In this study, we have resequenced the flanking and coding region of KCNJ5 in peripheral blood DNA from 251 white subjects with primary aldosteronism to look for rare variants that might be important for the pathophysiology of sporadic primary aldosteronism. We have identified 3 heterozygous missense mutations (R52H, E246K, and G247R) in the cohort and found that 12 (5% of the cohort) were carriers for the rare nonsynonymous single nucleotide polymorphism rs7102584 causing E282Q substitution of KCNJ5. By expressing the channels in Xenopus oocytes and human adrenal H295R cells, we have shown that the R52H, E246K, and E282Q substitutions are functional, but the G247R mutation is indistinguishable from wild type. Although the functional substitutions are remote from the selectivity filter, they affect the inward-rectification, the ability of the KCNJ5 channels to conduct Na(+) currents and ATII-induced aldosterone release from the H295R cell line. Together these data suggest that germline variation in the KCNJ5 gene has a role to play in the common sporadic form as well as the much rarer syndromic forms of primary aldosteronism.

Molecular genetic investigative leads to differentiate monozygotic twins.

Molecular genetic investigative leads to differentiate monozygotic twins.

Association of specific diplotypes defined by common rs1800682 and rare rs34995925 single nucleotide polymorphisms within the STAT1 transcription binding site of the FAS gene promoter with preeclampsia

The tolerance of fetal antigens by intradecidual T-cell involving the Fas-mediated apoptosis plays an important role in the physiological course of pregnancy. Objective of this study is to determine the association of diplotypes of common rs1800682G and rare rs34995925C alleles within the STAT1 transcription binding site of the FAS promoter region with preeclampsia. There were 116 preeclamptic women and 123 healthy control subjects from Hungary and Slovakia enrolled in the study. The presence of the GG or GA genotypes on rs1800682 was confirmed in 91 patients and 85 controls (OR = 1.628, 95%CI 0.907-2.92). The rare rs34995925 C allele laying 7 bp further from rs1800682 within STAT1 transcription binding site was detected in 3 preeclamptic cases and none healthy subjects. Haplotypes GT and AC were defined by common rs1800682G and rare rs34995925C alleles, respectively, and were considered as "low" FAS-producing. The combinations of GT or AC with normal FAS-producing haplotypes AT were considered as "low" FAS-producing diplotypes in dominant model. The "low" FAS -producing diplotype group of GT/GT, GT/AT, and AC/AT compared to the normal FAS-producing diplotype group of AT/AT showed OR = 1.91 (95%CI 1.04-3.48) and p = 0.03 for the association with preeclampsia.

A New System Identification Approach to Identify Genetic Variants in Sequencing Studies for a Binary Phenotype

We propose in this paper a set-valued (SV) system model, which is a generalized form of logistic (LG) and Probit (Probit) regression, to be considered as a method for discovering genetic variants, especially rare genetic variants in next-generation sequencing studies, for a binary phenotype. We propose a new SV system identification method to estimate all underlying key system parameters for the Probit model and compare it with the LG model in the setting of genetic association studies. Across an extensive series of simulation studies, the Probit method maintained type I error control and had similar or greater power than the LG method, which is robust to different distributions of noise: logistic, normal, or t distributions. Additionally, the Probit association parameter estimate was 2.7-46.8-fold less variable than the LG log-odds ratio association parameter estimate. Less variability in the association parameter estimate translates to greater power and robustness across the spectrum of minor allele frequencies (MAFs), and these advantages are the most pronounced for rare variants. For instance, in a simulation that generated data from an additive logistic model with an odds ratio of 7.4 for a rare single nucleotide polymorphism with a MAF of 0.005 and a sample size of 2,300, the Probit method had 60% power whereas the LG method had 25% power at the α = 10^-6 level. Consistent with these simulation results, the set of variants identified by the LG method was a subset of those identified by the Probit method in two example analyses. Thus, we suggest the Probit method may be a competitive alternative to the LG method in genetic association studies such as candidate gene, genome-wide, or next-generation sequencing studies for a binary phenotype.

Common and rare single nucleotide polymorphisms in the LDLR gene are present in a black South African population and associate with low-density lipoprotein cholesterol levels

The LDL receptor has an essential role in regulating plasma LDL-C levels. Genetic variation in the LDLR gene can be associated with either lower or moderately raised plasma levels of LDL-C, or may cause familial hypercholesterolemia. The prevalence of single-nucleotide polymorphisms (SNPs) in the LDLR in the black South African population is not known and therefore, we aimed to determine the genotypic variation of the LDLR in the study population as well as to define the association of the different genotypes with plasma LDL-C levels. A random selection of 1860 apparently healthy black South African volunteers aged 35-60 years was made in a cross-sectional study. Novel SNPs were identified in a subset of 30 individuals by means of automated sequencing before screening the entire cohort by means of the Illumina VeraCode GoldenGate Genotyping Assay on a BeadXpress Reader system. Twenty-five SNPs were genotyped, two of which were novel. A very rare SNP, rs17249141, in the promoter region was significantly associated with lower levels of LDL-C. Four other SNPs (rs2738447, rs14158, rs2738465 and rs3180023) were significantly associated with increased levels of LDL-C. We can conclude that some of the various SNPs identified do indeed associate with LDL-C levels.

Analysis For Loss Of 13q Heterozygosity Using STR Or SNP Analysis Can Replace Analysis Of FLT3-ITD To Detect Prognostically Adverse AML

BackgroundFLT3-ITD has been established as an adverse prognostic factor in acute myeloid leukemia (AML). However, it has been repeatedly shown that not the presence of FLT3-ITD by itself confers the unfavorable effect, but the excess load of the FLT3-ITD in comparison to the FLT3 wild-type (wt) allele, which occurs by loss of heterozygosity (LOH) due to somatic isodisomy of chromosome 13q. AimAs now analysis of FLT3-ITD in many countries is restricted by patent claims we aimed at developing a novel assay for LOH detection on 13q as a substitute for FLT3-ITD to identify patients (pts) with a higher risk for shorter survival. Patients and Methods1) First an intensively treated AML cohort with normal karyotype (NK) (n=453) was selected in which the FLT3-ITD/wt ratio was assessed by a standard procedure (fragment length analysis by gene scan). 2) In a second step, a subcohort (cohort 2) of 233/453 pts was analyzed for LOH in 13q by fragment analysis of polymorphic single tandem repeat (STR) markers flanking the FLT3 gene as previously described (Whitman et al., JCO 2001). 3) A further subset of 91 pts from cohort 2 was subjected to a proof-of-principle study of applying next generation amplicon sequencing (NGS) for detection of LOH using a combination of Access Arrays (Fluidigm, South San Francisco, CA) and the 250 bp paired-end read chemistry on a MiSeq instrument (Illumina, San Diego, CA). In total, 41 amplicons were designed covering 67 different known SNPs (single nucleotide polymorphisms), with 43 SNPs flanking the FLT3 gene in the telomeric and the centromeric direction (genomic position: chr13:26,755,356-38,231,018), 22 SNPs being located in FLT3 intronic regions and one SNP each in exons 2 and 6. The achieved median coverage per SNP was 6,143 reads (range 58 - 30,311). Results1) In the control cohort of 453 NK-AML (FLT3-ITD+: n=162, 35.8%) the adverse impact of high FLT3-ITD burden was reproduced. According to FLT3-ITD/FLT3wt a ratio of <0.5 was detected in n=60 (13.2%), between 0.5 and <1 in 69 (15.2%) and ≥1 in 33 (7.3%) cases. Survival in patients (pts) with a FLT3-ITD load <0.5 was not different from those with FLT3-wt (54% 3-year survival for both, p=n.s.). In contrast, the outcome in pts with a load of >1 (LOH) was significantly shorter as compared to all others (EFS: 3.6 vs 14.4 months, p<0.001, respectively). These results clearly show that 13q-LOH outperforms the presence of FLT3-ITD per se as a prognostic marker. 2) Therefore, we next performed the STR analysis in a subcohort of 233 pts (FLT3-ITD+ load >1: n=83, FLT3-ITD+ load ≤1: n=105, FLT3wt: n=45). The median mutation load was 0.80 (range: 0.03-181.7). In all patients at least one informative STR marker was identified: 1: n=6 pts, 2: n=23 pts, 3: n=60 pts, 4: n=77 pts, 5: n=67 pts). STR allele ratios were similar for FLT3wt and FLT3-ITD with burden of ≤1. A threshold of a STR aIlelic ratio ≥70% allows identification of 81/83 samples with LOH (positive detection: 97.6%). Median EFS was 4.7 months in the 13q LOH group compared to 14.4 months in all others (p=0.001), clearly demonstrating that STR analysis using five 13q-specific markers can be used as a powerful tool to generate prognostic data. 3) As the gene scan procedure was time consuming, we next tested whether an NGS-based high-throughput SNP analysis can detect the LOH cases with the same precision. In total, 110 different SNPs were detected in this cohort (43 more than the anticipated 67, as many pts had additional rare SNPs). Complete homozygous SNP constellations were regarded as not informative. A median of 67 SNPs/pts (range: 44-80) were detected with a median informative allele constellation of 51/pts (range: 27-70). The allelic SNP load was calculated from the mean allelic load of all informative SNPs and then correlated to the FLT3-ITD load as calculated by gene scan. Across the total subset of 91 pts a very good correlation was detected (Spearman, R=0.807, p<0.001). This was even better when only the cases with LOH, as assessed by the other two methods, were regarded (n=48, R=0.916, p<0.001). In total, 47/48 of the LOH pts were identified by this method showing a positive detection rate of 97.9%. Conclusions1) Not the presence of FLT3-ITD per se but a high FLT3-ITD load due to LOH of 13q has prognostically adverse impact. 2) Assessment of LOH can be done either by STR analysis or even more accessible by quantification of SNP allelic ratios using NGS amplicon deep-sequencing with a positive detection rate of 97.9%. Disclosures:Schnittger:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Weber:MLL Munich Leukemia Laboratory: Employment. Schindela:MLL Munich Leukemia Laboratory: Employment. Roller:MLL Munich Leukemia Laboratory: Employment. Alpermann:MLL Munich Leukemia Laboratory: Employment. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.