2008 Barcelona - European Society of Human Genetics

Concurrent Sessions
APC, BRCA1 and BRCA2. The protocol steps have been streamlined
for routine application as follows: 1) PCR amplification of the relevant
exon, including flanking intronic sequences, 2) cloning into a two-exon
splicing reporter minigene, 3) selection of wild-type- and variant-carrying
plasmids, 4) transfection into HeLa cells, 5) RNA extraction
and RT-PCR using primers targeting minigene sequences, and 6)
sequence analysis of all RT-PCR products . Variants associated with
total absence of correct exon inclusion in this monoallelic assay are
considered as most likely pathogenic but UVs inducing partial alterations
of normal mRNA sequences are also considered as biologically
significant. In spite of our initial concern that exons are tested in a heterologous
context, extensive comparisons with in vivo RNA data have
shown that this minigene-based approach is sensitive and specific.
Comparisons with results from in silico analysis indicate that current
bioinfomatic predictions are sensitive and rather specific concerning
changes in splice site strength, activation of cryptic sites or generation
of new splice sites, but are still inadequate for predicting the presence
of relevant exonic splicing regulatory elements .
c13.1
A genome-wide scan of adult human stature and skeletal size
N. Soranzo 1 , F. Rivadeneira 2 , U. Chinappen 3 , M. Inouye 1 , B. J. Richards 3 , S.
Potter 1 , R. Gwilliam 1 , K. Papadakis 4 , E. Wheeler 1 , I. Barroso 1 , D. Hart 5 , G.
Livshits 6 , R. J. F. Loos 7 , D. Strachan 4 , N. J. Wareham 7 , T. D. Spector 3 , A. Uitterlinden
2 , P. Deloukas 1 ;
1 The Wellcome Trust Sanger Institute, Hinxton, United Kingdom, 2 Erasmus
MC, Rotterdam, The Netherlands, 3 School of Medicine, King’s College London,
London, United Kingdom, 4 St George’s, University of London, London, United
Kingdom, 5 St. Thomas’ Hospital, London, United Kingdom, 6 Tel Aviv University,
Tel Aviv, Israel, 7 Institute of Metabolic Science, Cambridge, United Kingdom.
Human adult stature is a classical quantitative trait and a paradigm
for genetic association studies of quantitative trait variation . We have
carried out a meta-analysis of four genome-wide association scans
of stature produced using the Illumina HumanHap300 SNP panel in
10,050 adults from four population-based cohorts (TwinsUK, EPIC
Norfolk and 1958 Birth Cohort from the UK and the Rotterdam Study
from the Netherlands). We have identified eighteen loci showing association
with height with P-values of less than 10 -5 , which we have
brought forward for replication in an independent sample of 9,000 individuals
.
The signals identified provide strong evidence for replication in genomic
regions previously implicated in height, including HMGA2 (rs8756,
P-value = 5x10 -13 ) and GDF5-UQCC (rs4911494, P-value = 1 .5x10 -10 ) .
In addition, we have identified novel candidate genetic loci for human
height, some of which are in or near genes implicated in cellular growth
and development (HHIP, ADAMTSL3 and DLEU7) . In an attempt to
dissect the mechanisms underlying human growth, we have tested the
association of these novel candidate height loci with different measurements
of skeletal growth . Our results provide both novel and confirmatory
evidence for the implication of genes and pathways in human
growth, thus contributing to the understanding of the biological processes
underlying many common and severe human diseases .
c13.2
super-hotspots for meiotic Recombination in the Human
Genome
I. L. Berg, A. J. Webb, A. J. Jeffreys;
Department of Genetics, University of Leicester, Leicester LE1 7RH, United
Kingdom.
Homologous recombination is a vital process for ensuring proper chromosome
segregation during meiosis, as well as increasing diversity by
reshuffling haplotypes between generations. In this study, we analysed
Phase II HapMap data to identify autosomal regions showing extreme
breakdown of linkage disequilibrium (LD) . Sixteen of these regions were
selected for crossover analysis directly in sperm . All contained active
sperm hotspots, with similar characteristics as at previously studied
hotspots, i .e . normally-distributed crossover breakpoints within regions
1-2 kb wide . These new hotspots were on average 10 fold more active
than previously characterised autosomal hotspots and include the
most active crossover hotspots yet discovered in the human genome .
Their activity is however poorly predicted from LD data . Most crossovers
in these hotspots were simple, exchanging haplotypes within a single
interval between markers . However, 0 .3% of exchanges were more
complex, switching haplotypes at several intervals during an exchange
event . Most of these occurred within the boundaries of the hotspot while
22% occurred beyond the hotpot, implying a broader region involved
during intermediate stages of recombination . Several hotspots showed
crossover frequency variation between men, including two cases of
complete presence/absence polymorphism . Instances of extreme or
subtle biased gene conversion accompanying crossover were observed
within some hotspots, in some cases correlating with crossover frequency
variation between men . Curiously none of the most active hotpots
showed polymorphism or strongly biased conversion, in contrast to the
prediction that these hotpots should be the most vulnerable to attenuation/extinction
by meiotic drive in favour of recombination suppressors .
c13.3
A full survey of common copy number variation in the human
genome
R. Redon 1 , D. F. Conrad 1 , L. Feuk 2 , C. Lee 3 , S. W. Scherer 2 , M. E. Hurles 1 , N.
P. Carter 1 ;
1 Wellcome Trust Sanger Institute, Cambridge, United Kingdom, 2 The Hospital
for Sick Children, Toronto, ON, Canada, 3 Brigham and Women’s Hospital, Boston,
MA, United States.
Copy number variation (CNV) in the genome is extensive and yet is
grossly under-ascertained . As smaller CNVs are expected to be far
more numerous than larger CNVs, improved CNV detection resolution
will dramatically increase the numbers of known CNVs . The Genome
Structural Variation Consortium has performed comparative genome
hybridisation on a genome-wide set of tiling oligonucleotide arrays to
discover the majority of common copy number variants >500bp in size
in two populations with African and European ancestry . This set covers
the assayable portion of the human genome with 42,000,000 probes
with a median spacing of ~50bp . In addition we have generated data
on a single chimpanzee to provide information on the ancestral state
of observed variants . The results reveal, as expected, that previous
surveys captured only 5-10% of the CNVs within a single genome .
Because the boundaries of thousands of CNVs are defined precisely
by this probe set, we can identify accurately functional sequences included
in copy number variable regions . This provides new insights
into the mechanisms generating chromosomal rearrangements and
the biological functions of common CNVs .
c13.4
Gene expression variation from peripheral blood in the general
population - the KORA study
D. Mehta 1 , K. Heim 1 , T. Illig 2 , H. Wichmann 2,3 , T. Meitinger 1,4 , H. Prokisch 1,4 ;
1 Helmholtz Zentrum München - Institute of Human Genetics, Munich, Germany,
2 Helmholtz Zentrum München - Institute of Epidemiology, Munich, Germany,
3 Institute of Medical Informatics,Biometry and Epidemiology, LMU, Munich,
Germany, 4 Institute of Human Genetics, Klinikum rechts der Isar, Technical
University Munich, Munich, Germany.
Interrogation of gene expression variation in humans will provide better
understanding of functional genetic variation and help identify disease
variants . At present, the nature and extent of variation in transcript levels
across the entire genome is largely unknown .
We assessed normal variation in gene expression from 350 KORA
individuals, using the Illumina Human Ref-6 v2 whole genome microarray
. Special features of inter individual variation in peripheral blood
expression could be traced to gender and age differences . Several
significant age-related genes and distinct gender-specific gene signatures
were identified. Using the PAM algorithm, it was possible to
predict the gender with an accuracy of 98% .
Using available KORA Affymetrix 500k genotypes, we performed a
genome-wide association study to compare peripheral blood eQTLs
(Expression Quantitative trait loci) to published lymphocyte cell culture
eQTLs .
Expression data can be used to prioritize candidate genes with expression
levels significantly correlated to the trait. In this context, a recent
genome wide association study using the KORA population found the
most significant SNPs associated with urate levels mapped within an
uncharacterized carrier gene SLC2A9. Our analysis revealed a significant
association between SLC2A9 expression and urate levels (Doering
et al, Nature Genetics in print) .
Analysis of further candidate genes where genome-wide association
signals have been obtained is currently underway .