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Genome-wide genetic marker discovery and genotyping using next-generation sequencing,”
- Nature Reviews Genetics,
, 2011
"... Abstract | The advent of next-generation sequencing (NGS) has revolutionized genomic and transcriptomic approaches to biology. These new sequencing tools are also valuable for the discovery, validation and assessment of genetic markers in populations. Here we review and discuss best practices for s ..."
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Abstract | The advent of next-generation sequencing (NGS) has revolutionized genomic and transcriptomic approaches to biology. These new sequencing tools are also valuable for the discovery, validation and assessment of genetic markers in populations. Here we review and discuss best practices for several NGS methods for genome-wide genetic marker development and genotyping that use restriction enzyme digestion of target genomes to reduce the complexity of the target. These new methods -which include reduced-representation sequencing using reduced-representation libraries (RRLs) or complexity reduction of polymorphic sequences (CRoPS), restriction-site-associated DNA sequencing (RAD-seq) and low coverage genotyping -are applicable to both model organisms with high-quality reference genome sequences and, excitingly, to non-model species with no existing genomic data.
Rapid SNP discovery and genetic mapping using sequenced RAD markers
- PLoS ONE
, 2008
"... Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) ..."
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Cited by 39 (1 self)
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Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F2 individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a
Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels
- Nature Genetics
, 2013
"... Association mapping can quickly and efficiently dissect complex agronomic traits. Rapeseed is one of the most economically important polyploid oil crops, although its genome sequence is not yet published. In this study, a recently developed 60K Brassica Infiniumw SNP array was used to analyse an ass ..."
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Cited by 25 (2 self)
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Association mapping can quickly and efficiently dissect complex agronomic traits. Rapeseed is one of the most economically important polyploid oil crops, although its genome sequence is not yet published. In this study, a recently developed 60K Brassica Infiniumw SNP array was used to analyse an association panel with 472 accessions. The single-nucleotide polymorphisms (SNPs) of the array were in silicomapped using ‘pseu-domolecules ’ representative of the genomeof rapeseed to establish their hypothetical order and to perform associationmapping of seedweight and seedquality. As a result, two significant associations onA8andC3of Brassica napus were detected for erucic acid content, and the peak SNPs were found to be only 233 and 128 kb away from the key genes BnaA.FAE1 and BnaC.FAE1. BnaA.FAE1was also identified to be significantly associatedwith the oil content. Orthologues ofArabidopsis thalianaHAG1were identified close to four clus-ters of SNPs associated with glucosinolate content on A9, C2, C7 and C9. For seed weight, we detected two association signals on A7 and A9, which were consistent with previous studies of quantitative trait loci mapping. The results indicate that our association mapping approach is suitable for fine mapping of the complex traits in rapeseed. Key words: Brassica napus; association mapping; SNP; seed quality; seed weight
Clonal analysis using recombinant DNA probes from the X-chromosome." Cancer Res 47(18
, 1987
"... This article has been cited by 28 HighWire-hosted articles. Access the articles at: ..."
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This article has been cited by 28 HighWire-hosted articles. Access the articles at:
Random Amplified Polymorphic DNA (RAPD) markers
- Turk J Biol
, 2001
"... Abstract: Due to advances in molecular biology techniques, large numbers of highly informative DNA markers have been developed for the identification of genetic polymorphism. In the last decade, the random amplified polymorphic DNA (RAPD) technique based on the polymerase chain reaction (PCR) has be ..."
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Abstract: Due to advances in molecular biology techniques, large numbers of highly informative DNA markers have been developed for the identification of genetic polymorphism. In the last decade, the random amplified polymorphic DNA (RAPD) technique based on the polymerase chain reaction (PCR) has been one of the most commonly used molecular techniques to develop DNA markers. RAPD markers are amplification products of anonymous DNA sequences using single, short and arbitrary oligonucleotide primers, and thus do not require prior knowledge of a DNA sequence. Low expense, efficiency in developinga large number of DNA markers in a short time and requirement for less sophisticated equipment has made the RAPD technique valuable although reproducibility of the RAPD profile is still the centre of debate.
Reading between the LINEs: human genomic variation induced by LINE-1 retrotransposition
- Genome Res
, 2000
"... The insertion of mobile elements into the genome represents a new class of genetic markers for the study of human evolution. Long interspersed elements (LINEs) have amplified to a copy number of about 100,000 over the last 100 million years of mammalian evolution and comprise ∼15 % of the human geno ..."
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The insertion of mobile elements into the genome represents a new class of genetic markers for the study of human evolution. Long interspersed elements (LINEs) have amplified to a copy number of about 100,000 over the last 100 million years of mammalian evolution and comprise ∼15 % of the human genome. The majority of LINE-1 (L1) elements within the human genome are 5 truncated copies of a few active L1 elements that are capable of retrotransposition. Some of the young L1 elements have inserted into the human genome so recently that populations are polymorphic for the presence of an L1 element at a particular chromosomal location. L1 insertion polymorphisms offer several advantages over other types of polymorphisms for human evolution studies. First, they are typed by rapid, simple, polymerase chain reaction (PCR)-based assays. Second, they are stable polymorphisms that rarely undergo deletion. Third, the presence of an L1 element represents identity by descent, because the probability is negligible that two different young L1 repeats would integrate independently between the exact same two nucleotides. Fourth, the ancestral state of L1 insertion polymorphisms is known to be the absence of the L1 element, which can be used to root plots/trees of population relationships. Here we report the development of a PCR-based display for the direct identification of dimorphic L1 elements from the human genome. We have also developed PCR-based assays for the characterization of six polymorphic L1 elements within the human genome. PCR analysis of human/rodent hybrid cell line DNA samples showed that
Identity-by-descent filtering of exome sequence data identifies PIGV mutations in Hyperphosphatasia Mental Retardation Syndrome
- Nat Genet
, 2010
"... Motivation: Next-Generation Sequencing (NGS) and exome-capture technologies are currently revolutionizing the way geneticists screen for disease-causing mutations in rare Mendelian disorders. However, the identification of causal mutations is challenging due to the sheer number of variants that are ..."
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Motivation: Next-Generation Sequencing (NGS) and exome-capture technologies are currently revolutionizing the way geneticists screen for disease-causing mutations in rare Mendelian disorders. However, the identification of causal mutations is challenging due to the sheer number of variants that are identified in individual exomes. Although databases such as dbSNP or HapMap can be used to reduce the plethora of candidate genes by filtering out common variants, the remaining set of genes still remains on the order of dozens. Results: Our algorithm uses a non-homogeneous hidden Markov model (HMM) that employs local recombination rates to identify chromosomal regions that are identical by descent (IBD=2) in children of consanguineous or non-consanguineous parents solely based on genotype data of siblings derived from high-throughput sequencing platforms. Using simulated and real exome sequence data, we show that our algorithm is able to reduce the search space for the causative disease gene to a fifth or a tenth of the entire exome. Availability: The source code and tutorial are available at
Understanding Human DNA Sequence Variation at Pennsylvania State U niversity on M arch 1, 2014 http://jhered.oxfordjournals.org/ D ow nloaded from
, 1991
"... Over the past century researchers have identified normal genetic variation and studied that variation in diverse human populations to determine the amounts and distributions of that variation. That information is being used to develop an understanding of the demographic histories of the different po ..."
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Over the past century researchers have identified normal genetic variation and studied that variation in diverse human populations to determine the amounts and distributions of that variation. That information is being used to develop an understanding of the demographic histories of the different populations and the species as a whole, among other studies. With the advent of DNA-based markers in the last quarter century, these studies have accelerated. One of the challenges for the next century is to understand that variation. One component of that understanding will be population genetics. We present here examples of many of the ways these new data can be analyzed from a population perspective using results from our laboratory on multiple individual DNA-based polymorphisms, many clustered in haplotypes, studied in multiple populations representing all major geographic regions of the world. These data support an ‘‘out of Africa’ ’ hypothesis for human dispersal around the world and begin to refine the understanding of population structures and genetic relationships. We are also developing baseline information against which we can compare findings at different loci to aid in the identification of loci subject, now and in the past, to selection (directional or balancing). We do not yet have a comprehensive understanding of the extensive variation in the human genome, but some of that understanding is coming from population genetics.
MolKin v2.0: A Computer Program for Genetic Analysis of Populations Using Molecular Coancestry Information.
- Journal of Heredity
, 2005
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M: Identification of an abnormal gene for the GPIIIa subunit of the platelet fibrinogen receptor resulting in Glanzmann’s thrombasthenia. Blood 75:881
, 1990
"... The platelet fibrinogen receptor, which is composed of glycoproteins Ilb (GPllb) and llla (GPllla), belongs to a large family of receptors that participate in a multitude of biologically important adhesive interactions. Platelets from most patients with the autosomal recessive bleeding disorder, Gla ..."
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Cited by 8 (2 self)
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The platelet fibrinogen receptor, which is composed of glycoproteins Ilb (GPllb) and llla (GPllla), belongs to a large family of receptors that participate in a multitude of biologically important adhesive interactions. Platelets from most patients with the autosomal recessive bleeding disorder, Glanzmann‘s thrombasthenia, are deficient in GPllb and GPllla. We have used cDNA probes to analyze the GPllb and GPllla genes in four patients from three kindreds with Glanzmann’s thrombasthenia. Southern analysis of their DNA was identical to that observed in normals when probed with a full-length GPllb cDNA or a 3 ‘ GPllla cDNA. However, in one family, a 5 ’ 2.0 kb GPllla cDNA identified abnormal DNA fragments in the father and two affected siblings ’ genes. A series of restriction digests resulting in small genomic fragments were probed with portions of the
