- Institute of Animal Sciences
ARO, The Volcani Center
P. O. Box 6
Bet Dagan 50250
Israel - 972-8-9484430
- B. Sc. in biology, Hebrew University of Jerusalem, 1974 M. Sc. in Genetics, Hebrew University of Jerusalem, 1976 Ph. ... moreB. Sc. in biology, Hebrew University of Jerusalem, 1974
M. Sc. in Genetics, Hebrew University of Jerusalem, 1976
Ph. D. in applied Genetics, Hebrew University of Jerusalem, 1984
Postdoctorate in animal breeding, Cornell University, 1982
Postdoctorate in animal breeding, ARS-USDA, 1982-1983edit
In accordance with the infinitesimal model for quantitative traits, a very large number of genes affect nearly all economic traits. In only two cases has the causative polymorphism been determined for genes affecting economic traits in... more
In accordance with the infinitesimal model for quantitative traits, a very large number of genes affect nearly all economic traits. In only two cases has the causative polymorphism been determined for genes affecting economic traits in dairy cattle. Most current methods for genomic evaluation are based on the "two-step" method. Genetic evaluations are computed by the individual animal model, and functions of the evaluations of progeny-tested sires are the dependent variable for estimation of marker effects. With the adoption of genomic evaluation in 2008, annual rates of genetic gain in the US increased from ∼50-100% for yield traits and from threefold to fourfold for lowly heritable traits, including female fertility, herd-life and somatic cell concentration. Gradual elimination of the progeny test scheme has led to a reduction in the number of sires with daughter records and less genetic ties between years. As genotyping costs decrease, the number of cows genotyped will continue to increase, and these records will become the basic data used to compute genomic evaluations, most likely via application of "single-step" methodologies. Less emphasis in selection goals will be placed on milk production traits, and more on health, reproduction, and efficiency traits and "environmentally friendly" production. Genetic variance for economic traits is maintained by increase in frequency of rare alleles, new mutations, and changes in selection goals and management.
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Forty-seven poly-TG microsatellites were developed at the U of IL, and 11 genetic markers were developed at ARO, nine of which were poly-AGC microsatellites. Markers were typed on the reference families of CSIRO, Australia; GRANADA,... more
Forty-seven poly-TG microsatellites were developed at the U of IL, and 11 genetic markers were developed at ARO, nine of which were poly-AGC microsatellites. Markers were typed on the reference families of CSIRO, Australia; GRANADA, Texas; and IRRF, Illinois, for chromosome assignment and linkage mapping. Nine North American al organizations contributed semen to the Dairy Bull DNA Repository (DBDR), which currently has 65,743 units from 3366 bulls. Semen was obtained for 31 out of 35 grandsires. Semen of 28 and 23 sons of two Israeli bulls was also collected. Eighteen grandsires were genotyped for 75 microsatellites. One thousand, three hundred and sixty-two sons with evaluation from 17 families were genotyped for 24 markers. Eleven thousand, six hundred and twenty sons genotypes were determined, of which 8,802 were informative. The genotype data was matched to the bulls' daughter yield deviations (DYD) for seven traits; milk, fat, and protein production; fat and protein percent...
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sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia (Oreochromis niloticus) Eshel et al. Eshel et al. BMC Genomics 2014, 15:774
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Analytical formulae are derived for the confidence interval for location of a quantitative trait locus (QTL) using a saturated genetic map, as a function of the experimental design, the QTL allele substitution effect, and the number of... more
Analytical formulae are derived for the confidence interval for location of a quantitative trait locus (QTL) using a saturated genetic map, as a function of the experimental design, the QTL allele substitution effect, and the number of individuals genotyped and phenotyped. The formulae are derived assuming evenly spaced recombination events, rather than the actual unevenly spaced distribution. The formulae are useful for determining desired sample size when designing a wide variety of QTL mapping experiments, and for evaluating a priori the potential of a given mapping population for defining the location of a QTL. The formulae do not take into account the finite number of recombination events in a given sample.
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Phenotypic and genetic changes for female fertility and production traits in the Israeli Holstein population over the last three decades were studied in order to determine if long term selection has resulted in reduced heritability and... more
Phenotypic and genetic changes for female fertility and production traits in the Israeli Holstein population over the last three decades were studied in order to determine if long term selection has resulted in reduced heritability and negative genetic correlations. Annual means for conception status, defined as the inverse of the number of inseminations to conception in percent, decreased from 55.6 for cows born in 1983 to 46.5 for cows born in 2018. Mean estimated breeding values increased by 1.8% for cow born in 1981 to cows born in 2018. Phenotypic records from 1988 to 2016 for the nine Israeli breeding index traits were divided into three time periods for multi-trait REML analysis by the individual animal model. For all traits, heritabilities increased or stayed the same for the later time periods. Heritability for conception status was 0.05. The first parity genetic correlation between conception status and protein yield was −0.38. Heritabilities decreased with the increase in...
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The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy... more
The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that...
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The main objectives of this research was to detect the specific polymorphisms responsible for observed quantitative trait loci and develop optimal strategies for genomic evaluations and selection for moderate (Israel) and large (US) dairy... more
The main objectives of this research was to detect the specific polymorphisms responsible for observed quantitative trait loci and develop optimal strategies for genomic evaluations and selection for moderate (Israel) and large (US) dairy cattle populations. A joint evaluation using all phenotypic, pedigree, and genomic data is the optimal strategy. The specific objectives were: 1) to apply strategies for determination of the causative polymorphisms based on the “a posteriori granddaughter design” (APGD), 2) to develop methods to derive unbiased estimates of gene effects derived from SNP chips analyses, 3) to derive optimal single-stage methods to estimate breeding values of animals based on marker, phenotypic and pedigree data, 4) to extend these methods to multi-trait genetic evaluations and 5) to evaluate the results of long-term genomic selection, as compared to traditional selection. Nearly all of these objectives were met. The major achievements were: The APGD and the modified...
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<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in... more
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle"http://www.biomedcentral.com/1471-2164/8/183BMC Genomics 2007;8():183-183.Published online 20 Jun 2007PMCID:PMC1906769.
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in... more
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle"http://www.biomedcentral.com/1471-2164/8/183BMC Genomics 2007;8():183-183.Published online 20 Jun 2007PMCID:PMC1906769.
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in... more
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle"http://www.biomedcentral.com/1471-2164/8/183BMC Genomics 2007;8():183-183.Published online 20 Jun 2007PMCID:PMC1906769.
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in... more
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle"http://www.biomedcentral.com/1471-2164/8/183BMC Genomics 2007;8():183-183.Published online 20 Jun 2007PMCID:PMC1906769.
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in... more
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle"http://www.biomedcentral.com/1471-2164/8/183BMC Genomics 2007;8():183-183.Published online 20 Jun 2007PMCID:PMC1906769.
Background: Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV’s potential as a major source for heritable variation in complex traits. Genomic selection... more
Background: Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV’s potential as a major source for heritable variation in complex traits. Genomic selection is a newly developed tool based on the estimation of breeding values for quantitative traits through the use of genome-wide genotyping of SNPs. Over 30,000 Holstein bulls have been genotyped with the Illumina BovineSNP50 BeadChip, which includes 54,001 SNPs (~SNP/50,000 bp), some of which fall within CNV regions. Results: We used the BeadChip data obtained for 912 Israeli bulls to investigate the effects of CNV on SNP calls. For each of the SNPs, we estimated the frequencies of occurrence of loss of heterozygosity (LOH) and of gain, based either on deviation from the expected Hardy-Weinberg equilibrium (HWE) or on signal intensity (SI) using the PennCNV “detect ” option. Correlations between LOH/CNV frequencies predicted by the two methods were low ...
Yearling weight gain in male and female Israeli Holstein calves, defined as 365 × ((weight − 35)/age at weight) + 35, was analyzed from 814,729 records on 368,255 animals from 740 herds recorded between 1994 and 2021. The variance... more
Yearling weight gain in male and female Israeli Holstein calves, defined as 365 × ((weight − 35)/age at weight) + 35, was analyzed from 814,729 records on 368,255 animals from 740 herds recorded between 1994 and 2021. The variance components were calculated based on valid records from 2008 through 2017 for each sex separately and both sexes jointly by a single-trait individual animal model analysis, which accounted for repeat records on animals. The analysis model also included the square root, linear, and quadratic effects of age at weight. Heritability and repeatability were 0.35 and 0.71 in the analysis of both sexes and similar in the single sex analyses. The regression of yearling weight gain on birth date in the complete data set was −0.96 kg/year. The complete data set was also analyzed by the same model as the variance component analysis, including both sexes and accounting for differing variance components for each sex. The genetic trend for yearling weight gain, including ...
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A method is described on the basis of a modification of the granddaughter design to obtain estimates of quantitative trait loci (QTL) allele frequencies in dairy cattle populations and to determine QTL genotypes for both homozygous and... more
A method is described on the basis of a modification of the granddaughter design to obtain estimates of quantitative trait loci (QTL) allele frequencies in dairy cattle populations and to determine QTL genotypes for both homozygous and heterozygous grandsires. The method is based on determining the QTL allele passed from grandsires to their maternal granddaughters using haplotypes consisting of several closely linked genetic markers. This method was applied to simulated data of 10 grandsire families, each with 500 granddaughters, and a QTL with a substitution effect of 0.4 phenotypic standard deviations and to actual data for a previously analyzed QTL in the center of chromosome 6, with substitution effect of 1 phenotypic standard deviation on protein percentage. In the simulated data the standard error for the estimated QTL substitution effect with four closely linked multiallelic markers was only 7% greater than the expected standard error with completely correct identification of...
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A total of 1922 first generation crossbred cows born between 2005 and 2012 produced by inseminating purebred Israeli Holstein cows with Norwegian Red semen, and 7487 purebred Israeli Holstein cows of the same age in the same 50 herds were... more
A total of 1922 first generation crossbred cows born between 2005 and 2012 produced by inseminating purebred Israeli Holstein cows with Norwegian Red semen, and 7487 purebred Israeli Holstein cows of the same age in the same 50 herds were analyzed for production, calving traits, fertility, calving diseases, body condition score, abortion rate and survival under intensive commercial management conditions. Holstein cows were higher than crossbreds for 305-day milk, fat and protein production. Differences were 764, 1244, 1231 for kg milk; 23.4, 37.4, 35.6 for kg fat, and 16.7, 29.8, 29.8 for kg protein; for parities 1 through 3. Differences for fat concentration were not significant; while crossbred cows were higher for protein concentration by 0.06% to 0.08%. Differences for somatic cells counts were not significant. Milk production persistency was higher for Holstein cows by 5, 8.3 and 8% in parities 1 through 3. Crossbred cows were higher for conception status by 3.1, 3.6 and 4.7% i...
Research Interests: Animal Science, Biology, Medicine, Biological Sciences, Animal, and 3 moreHERD, Metritis, and Crossbreed
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We present a simple algorithm for reconstruction of haplotypes from a sample of multilocus genotypes. The algorithm is aimed specifically for analysis of very large pedigrees for small chromosomal segments, where recombination frequency... more
We present a simple algorithm for reconstruction of haplotypes from a sample of multilocus genotypes. The algorithm is aimed specifically for analysis of very large pedigrees for small chromosomal segments, where recombination frequency within the chromosomal segment can be assumed to be zero. The algorithm was tested both on simulated pedigrees of 155 individuals in a family structure of three generations and on real data of 1149 animals from the Israeli Holstein dairy cattle population, including 406 bulls with genotypes, but no females with genotypes. The rate of haplotype resolution for the simulated data was >91% with a standard deviation of 2%. With 20% missing data, the rate of haplotype resolution was 67.5% with a standard deviation of 1.3%. In both cases all recovered haplotypes were correct. In the real data, allele origin was resolved for 22% of the heterozygous genotypes, even though 70% of the genotypes were missing. Haplotypes were resolved for 36% of the males. Com...
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Estimates of quantitative trait loci (QTL) effects derived from complete genome scans are biased, if no assumptions are made about the distribution of QTL effects. Bias should be reduced if estimates are derived by maximum likelihood,... more
Estimates of quantitative trait loci (QTL) effects derived from complete genome scans are biased, if no assumptions are made about the distribution of QTL effects. Bias should be reduced if estimates are derived by maximum likelihood, with the QTL effects sampled from a known distribution. The parameters of the distributions of QTL effects for nine economic traits in dairy cattle were estimated from a daughter design analysis of the Israeli Holstein population including 490 marker-by-sire contrasts. A separate gamma distribution was derived for each trait. Estimates for both the α and β parameters and their SE decreased as a function of heritability. The maximum likelihood estimates derived for the individual QTL effects using the gamma distributions for each trait were regressed relative to the least squares estimates, but the regression factor decreased as a function of the least squares estimate. On simulated data, the mean of least squares estimates for effects with nominal 1% s...
Research Interests: Evolutionary Biology, Algorithms, Biology, Breeding, Infertility, and 15 moreMedicine, Biological Sciences, Maximum Likelihood, Female, Animals, Male, Estimation, Heritability, Phenotype, Cattle, Dairy Cattle, Quantitative Trait Loci, Coefficient of Determination, Likelihood Functions, and Gamma Distribution
Ana posteriorigranddaughter design was applied to estimate quantitative trait loci genotypes of sires with many sons in the US Holstein population. The results of this analysis can be used to determine concordance between specific... more
Ana posteriorigranddaughter design was applied to estimate quantitative trait loci genotypes of sires with many sons in the US Holstein population. The results of this analysis can be used to determine concordance between specific polymorphisms and segregating quantitative trait loci. Determination of the actual polymorphisms responsible for observed genetic variation should increase the accuracy of genomic evaluations and rates of genetic gain. A total of 52 grandsire families, each with ⩾100 genotyped sons with genetic evaluations based on progeny tests, were analyzed for 33 traits (milk, fat and protein yields; fat and protein percentages; somatic cell score (SCS); productive life; daughter pregnancy rate; heifer and cow conception rates; service-sire and daughter calving ease; service-sire and daughter stillbirth rates; 18 conformation traits; and net merit). Of 617 haplotype segments spanning the entire bovine genome and each including ~5×106bp, 5 cM and 50 genes, 608 autosomal...
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The objectives were to continue collection of semen for the US dairy bull DNA repository, to conduct a systematic search of the Holstein genome for economically significant economic trait loci (ETL), to develop and refine statistical... more
The objectives were to continue collection of semen for the US dairy bull DNA repository, to conduct a systematic search of the Holstein genome for economically significant economic trait loci (ETL), to develop and refine statistical techniques for the analysis of the data generated, and to confirm significant effects by genotyping daughters i Israel and additional US sons. One-thousand-seventy-six sons of eight US grandsires were genotyped for 174 microsatellites located on all 29 autosomes. ETL were detected for milk production traits on seven chromosomes. ETL for milk and fat yield and fat and protein percentage on BTA3 was mapped to between the markers BL41 and TGLA263. The 95% confidence interval for the ETL affecting fat percentage on BTA14 localized this ETL between the contromere and chromosome position 11 cM. This ETL was verified in the Israeli cattle population by genotyping an independent sample of cows from seven families. The radiation hybrid data for the centromeric r...
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Individual loci affecting economic traits in dairy cattle (ETL) have been detected via linkage to genetic markers by application of the granddaughter design in the US population and the daughter design in the Israeli population. From... more
Individual loci affecting economic traits in dairy cattle (ETL) have been detected via linkage to genetic markers by application of the granddaughter design in the US population and the daughter design in the Israeli population. From these analyses it is not possible to determine allelic frequencies in the population at large, or whether the same alleles are segregating in different families. We proposed to answer this question by application of the "modified granddaughter design", in which granddaughters with a common maternal grandsire are both genotyped and analyzed for the economic traits. The objectives of the proposal were: 1) to fine map three segregating ETL previously detected by a daughter design analysis of the Israeli dairy cattle population; 2) to determine the effects of ETL alleles in different families relative to the population mean; 3) for each ETL, to determine the number of alleles and allele frequencies. The ETL on Bostaurusautosome (BT A) 6 chiefly af...
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Sequences of primers for 8 polymorphic markers on LG12. <br>Assembled genomic sequences of <i>GADD45G</i>-like gene locus of <i>P. reticulata</i>. Translated coding sequence (upper case) of the 151 (in... more
Sequences of primers for 8 polymorphic markers on LG12. <br>Assembled genomic sequences of <i>GADD45G</i>-like gene locus of <i>P. reticulata</i>. Translated coding sequence (upper case) of the 151 (in reverse orientation, blue) and the 137 (yellow) amino-acid isoforms are annotated.<br>
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in... more
<b>Copyright information:</b>Taken from "Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle"http://www.biomedcentral.com/1471-2164/8/183BMC Genomics 2007;8():183-183.Published online 20 Jun 2007PMCID:PMC1906769.
Three methods were tested to select subsets of markers from the Illumina BovineSNP50 BeadChip to compute genomic evaluations for moderately sized dairy cattle populations with ~1000 genotyped bulls. SNPs were selected based on: (1) their... more
Three methods were tested to select subsets of markers from the Illumina BovineSNP50 BeadChip to compute genomic evaluations for moderately sized dairy cattle populations with ~1000 genotyped bulls. SNPs were selected based on: (1) their effects on the bulls’ genetic evaluations for protein production in 2009 through 2013, as derived by the “EMMAX” algorithm including only bulls with daughter records; (2) their effects in the 2009 evaluations, also including bulls without daughter records; and (3) the regression of the SNPs allelic frequency on the bulls' birth dates. Milk, fat, and protein yield, somatic cell score, fertility, persistency, herd-life and the Israeli breeding index were analyzed by methods 2 and 3. Once SNPs were selected, only information available in 2009 was used to compute genomic evaluations for the validation bulls, who did not have daughter records in 2009. The optimum number of SNPs, as determined by correlations between genomic and 2013 evaluations, rang...
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Datasets of US and Israeli Holsteins were used to evaluate the impact of older generations on ability to predict EBV of young genotyped animals in traditional and single-step genomic BLUP. Inclusion of two (A2) or all (Af) ancestor... more
Datasets of US and Israeli Holsteins were used to evaluate the impact of older generations on ability to predict EBV of young genotyped animals in traditional and single-step genomic BLUP. Inclusion of two (A2) or all (Af) ancestor generations was also evaluated. A total of 34,506 US and 1,305 Israeli bulls were genotyped. Thresholds for data deletion were based on 5 years interval. The number of generations deleted without reduction in accuracy depended on data structure and trait. For US Holsteins, removing 3 and 4 generations of data did not reduce accuracy for final score in Af and A2, respectively. For Israeli Holsteins, the effect of removing older generations depended on the genetic origins of the bulls. Therefore, truncating older data does not decrease the accuracy of young genotyped bulls, while reducing computation requirements and helping to find problems in the population structure.
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Investment in breeding is unique because genetic gains are eternal and cumulative. They are never “used up”, and never “wear out”. However, nearly all of the gain is transferred to the national economy. Very little stays with farmers or... more
Investment in breeding is unique because genetic gains are eternal and cumulative. They are never “used up”, and never “wear out”. However, nearly all of the gain is transferred to the national economy. Very little stays with farmers or commercial breeders. Unlike genetic gains, costs are not cumulative. With a profit horizon of 20 years and a discount rate of 0.08, total dis- counted costs will equal total discounted gains if the value of the nominal annual genetic gains is 0.3 of the nominal annual costs. The rate of genetic gain for milk production in dairy cattle has been about 1% per year for the last 20 years. Since the 1950s, rates of genetic gain have increased due to better pedigree information, more traits recorded, more accurate recording, and better statistical methods. From the beginning of modern breeding programs, selection in dairy cattle focused on milk production. From 1985, breeding goals moved towards improving protein yield. In recent years, selection objectives...
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Many studies have proposed that rates of genetic gain in dairy cattle can be increased by direct selection on the individual quantitative loci responsible for the genetic variation in these traits, or selection on linked genetic markers.... more
Many studies have proposed that rates of genetic gain in dairy cattle can be increased by direct selection on the individual quantitative loci responsible for the genetic variation in these traits, or selection on linked genetic markers. The development of DNA-level genetic markers has made detection of QTL nearly routine in all major livestock species. The studies that attempted to detect genes affecting quantitative traits can be divided into two categories: analysis of candidate genes, and genome scans based on within-family genetic linkage. To date, 12 patent cooperative treaty (PCT) and US patents have been registered for DNA sequences claimed to be associated with effects on economic traits in dairy cattle. All claim effects on milk production, but other traits are also included in some of the claims. Most of the sequences found by the candidate gene approach are of dubious validity, and have been repeated in only very few independent studies. The two missense mutations on chr...
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ABSTRACT