James M. Farnham

A candidate prostate cancer susceptibility gene at chromosome 17p

It is difficult to identify genes that predispose to prostate cancer due to late age at diagnosis, presence of phenocopies within high-risk pedigrees and genetic complexity. A genome-wide scan of large, high-risk pedigrees from Utah has provided evidence for linkage to a locus on chromosome 17p. We carried out positional cloning and mutation screening within the refined interval, identifying a gene, ELAC2, harboring mutations (including a frameshift and a nonconservative missense change) that segregate with prostate cancer in two pedigrees. In addition, two common missense variants in the gene are associated with the occurrence of prostate cancer. ELAC2 is a member of an uncharacterized gene family predicted to encode a metal-dependent hydrolase domain that is conserved among eukaryotes, archaebacteria and eubacteria. The gene product bears amino acid sequence similarity to two better understood protein families, namely the PSO2 (SNM1) DNA interstrand crosslink repair proteins and the 73-kD subunit of mRNA 3′ end cleavage and polyadenylation specificity factor (CPSF73).

Can standard measures identify subclinical markers of autism

This study compared the executive function and theory-of-mind abilities of siblings of autistic individuals to those of siblings of learning-disabled controls. Three different analyses of the dependent measures provided convergent support for a potential subclinical marker in the executive function domain. No group differences in theory-of-mind abilities were found. However, power analyses revealed that the measures employed in this study, which are typically used with autistic individuals, were not sufficiently sensitive to detect any group differences that might exist in “unaffected” family members. Suggestions for future research are provided, including the need to develop more sensitive tasks that produce larger effects and measure more elementary cognitive operations.

Evidence for an inherited predisposition contributing to the risk for rotator cuff disease.

BACKGROUND A genetic predisposition has been suggested to contribute to the risk for development of rotator cuff disease on the basis of observed family clusters of close relatives. We used a population-based resource combining genealogical data for Utah with clinical diagnosis data from a large Utah hospital to test the hypothesis of excess familial clustering for rotator cuff disease. METHODS The Utah Population Database contains combined health and genealogical data on over two million Utah residents. Current Procedural Terminology, Fourth Revision, codes (29827, 23412, 23410, and 23420) and International Classification of Diseases, Ninth Revision, codes (726.1, 727.61, and 840.4) entered in patient records were used to identify patients with rotator cuff disease. We tested the hypothesis of excess familial clustering using two well-established methods (the Genealogical Index of Familiality test and the estimation of relative risks in relatives) in the overall study group (3091 patients) and a subgroup of the study group diagnosed before the age of forty years (652 patients). RESULTS The Genealogical Index of Familiality test in patients diagnosed before the age of forty years showed significant excess relatedness for individuals with rotator cuff disease in close and distant relationships (as distant as third cousins) (p = 0.001). The relative risk of rotator cuff disease in the relatives of patients diagnosed before the age of forty years was significantly elevated for second degree (relative risk = 3.66, p = 0.0076) and third degree (relative risk = 1.81, p = 0.0479) relatives. CONCLUSIONS We analyzed a set of patients with diagnosed rotator cuff disease and a known genealogy to describe the familial clustering of affected individuals. The observations of significant excess relatedness of patients and the significantly elevated risks to both close and distant relatives of patients strongly support a heritable predisposition to rotator cuff disease.

Shared genomic segment analysis. Mapping disease predisposition genes in extended pedigrees using SNP genotype assays.

We examine the utility of high density genotype assays for predisposition gene localization using extended pedigrees. Results for the distribution of the number and length of genomic segments shared identical by descent among relatives previously derived in the context of genomic mismatch scanning are reviewed in the context of dense single nucleotide polymorphism maps. We use long runs of loci at which cases share a common allele identically by state to localize hypothesized predisposition genes. The distribution of such runs under the hypothesis of no genetic effect is evaluated by simulation. Methods are illustrated by analysis of an extended prostate cancer pedigree previously reported to show significant linkage to chromosome 1p23. Our analysis establishes that runs of simple single locus statistics can be powerful, tractable and robust for finding DNA shared between relatives, and that extended pedigrees offer powerful designs for gene detection based on these statistics.

Correcting for multiple analyses in genomewide linkage studies.

The dissection of complex traits frequently calls for multiple analyses to be performed, including the use of both multiple phenotypes and genetic models. These multiple phenotypes and models are often not independent, and hence the necessary correction for the multiple testing is not straightforward. In this paper we offer a new approach to address the problem of how to correct for non‐independent multiple analyses in genomewide linkage studies. We describe one method of how to determine the number of ‘effectively independent’ tests performed in a linkage study using simple linear regression techniques. Further we describe how to use such information to establish genomewide significance thresholds for infinitely dense genomewide maps.

Novel popout: empirical boundaries and tentative theory

Observers received glimpses of 4-word arrays and were probed for the locations of particular words. Familiar words were repeated across arrays but novel words were not. Accuracy was higher for familiar than for novel arrays, but this baseline difference was diminished when a single novel word appeared with three familiar words. In these arrays, accuracy rose above baseline for novel words, defining novel popout (NPO), and fell below baseline for familiar words, defining familiar sink-in (FSI). In Experiments 1-4, these effects increased directly with field familiarity and associative unitization. In Experiments (-e, NPO remained intact and FSI actually increased as duration of array exposure was reduced from 200 ms to as brief as 33 ms. At brief exposures, even familiar words popped out from fields in which they had never before appeared

Significant Linkage Evidence for a Predisposition Gene for Pelvic Floor Disorders on Chromosome 9q21

Predisposition factors for pelvic floor disorders (PFDs), including pelvic organ prolapse (POP), stress urinary incontinence (SUI), urge urinary incontinence (UUI), and hernias, are not well understood. We assessed linkage evidence for PFDs in mostly sister pairs who received treatment for moderate-to-severe POP. We genotyped 70 affected women of European descent from 32 eligible families with at least two affected cases by using the Illumina 1 million single-nucleotide polymorphism (SNP) marker set. Parametric linkage analysis with general dominant and recessive models was performed by the Markov chain Monte Carlo linkage analysis method, MCLINK, and a set of SNPs was formed, from which those in high linkage disequilibrium were eliminated. Significant genome-wide evidence for linkage was identified on chromosome 9q21 with a HLOD score of 3.41 under a recessive model. Seventeen pedigrees (53%) had at least nominal evidence for linkage on a by-pedigree basis at this region. These results provide evidence for a predisposition gene for PFDs on chromosome 9q.

Replication of the 10q11 and Xp11 Prostate Cancer Risk Variants: Results from a Utah Pedigree-Based Study

A recent genome-wide association study suggested seven new loci as associated with prostate cancer susceptibility. The strongest associated single nucleotide polymorphism (SNP) in each region was identified (rs2660753, rs9364554, rs6465657, rs10993994, rs7931342, rs2735839, rs5945619). We studied these seven SNPs in a replication study consisting of 169 familial prostate cancer cases selected from Utah high-risk prostate cancer pedigrees and 805 controls. We performed subset analyses for aggressive and early-onset prostate cancer. At a nominal significance level, two SNPs were found to be associated with prostate cancer: rs10993994 on chromosome 10q11 [odds ratio (OR), 1.42; 95% confidence interval (95% CI), 1.05-1.90; P = 0.022] and rs5945619 on chromosome Xp11 (OR, 1.54; 95% CI, 1.03-2.31; P = 0.035). Restricting analysis to familial prostate cancer cases with aggressive disease yielded very similar risk estimates at both SNPs. However, subset analysis for familial, early-onset disease indicated highly significant association evidence and substantially higher risk estimates for rs10993994 (OR, 2.20; 95% CI, 1.48-3.27; P < 0.0001). This result suggests that the higher risk estimates from the stage 1 cohort in the original study for rs10993994 may have been due to the early-onset and familial nature of the prostate cancer cases in that cohort. In conclusion, in a small case-control study of prostate cancer cases from Utah high-risk pedigrees, we have significantly replicated association of prostate cancer with rs10993994 (10q11) upon study-wide correction for multiple comparisons. We also nominally replicated the association of prostate cancer with rs5945619 (Xp11). In particular, it seems that the susceptibility locus at 10q11 maybe involved in familial, early-onset disease. (Cancer Epidemiol Biomarkers Prev 2009;18(4):1290–4)

Confirmation of the HPCX prostate cancer predisposition locus in large Utah prostate cancer pedigrees

Several genetic predisposition loci for prostate cancer have been identified through linkage analysis, and it is now generally recognized that no single gene is responsible for more than a small proportion of prostate cancers. However, published confirmations of these loci have been few, and failures to confirm have been frequent. The genetic etiology of prostate cancer is clearly complex and includes significant genetic heterogeneity, phenocopies, and reduced penetrance. Powerful analyses that involve robust statistics and methods to reduce genetic heterogeneity are therefore necessary. We have performed linkage analysis on 143 Utah pedigrees for the previously published Xq27-28 (HPCX) prostate cancer susceptibility locus. We employed a robust multipoint statistic (TLOD) and a novel splitting algorithm to reduce intra-familial heterogeneity by iteratively removing the top generation from the large Utah pedigrees. In a dataset containing pedigrees having no more than five generations, we observed a multipoint TLOD of 2.74 (P=0.0002), which is statistically significant after correction for multiple testing. For both the full-structure pedigrees (up to seven generations) and the smaller sub-pedigrees, the linkage evidence was much reduced. This study thus represents the first significant confirmation of HPCX (Xq27-28) and argues for the continued utility of large pedigrees in linkage analyses for complex diseases.

Novel popout with nonsense strings: Effects of predictability of string length and spatial location

Recent studies have shown that when one of four expected words is replaced by a single unexpected word, the unexpected word may capture attention. In three experiments, we explored the generality of this effect. In each experiment, observers viewed arrays composed of four computergenerated “nonsense” strings. Accuracy of string localization was assessed after each array. Some strings, calledfamiliar, appeared in many arrays, whereas others, callednovel, appeared in only one. In each experiment, novel strings in arrays composed of one novel and three familiar strings were localized more accurately than were novel strings in arrays composed entirely of novel strings, and familiar strings in these arrays were localized less accurately than were familiar strings in arrays composed entirely of familiar strings. These two effects, termednovel popout andfamiliar sink-in, respectively, were observed even when novel and familiar strings were rendered less discriminable by holding their lengths constant (Experiment 2) and when familiar strings always appeared in the same spatial locations (Experiment 3). The data suggest that novel objects can capture attention even when the objects lack any clear linguistic referent, when they are superficially similar to the familiar objects that surround them, and when the spatial locations of familiar objects are completely predictable.