http://www.ncbi.nlm.nih.gov/sites/books/NBK158900/
./sratoolkit.2.4.2-ubuntu64/bin/fastq-dump --split-3 -L info --gzip -v SRR1131659
Showing posts with label sequencing. Show all posts
Showing posts with label sequencing. Show all posts
Tuesday, December 16, 2014
Monday, July 14, 2014
UBC Pharmaceutical Sequencing Centre - HiSeq 2500 and MiSeq
http://psas.pharmacy.ubc.ca/equipment/illumina-hiseq-2500-and-miseq/
Pricing
HiSeq Rapid Run 2×100: 375-425k clusters/mm2, 50-60 Gb data, 600 million reads – $2,400
HiSeq High Output 2×100: 375k-425k clusters/mm2, 33-40 Gb data, 37.5 million reads – $2,400
Pricing
HiSeq Rapid Run 2×100: 375-425k clusters/mm2, 50-60 Gb data, 600 million reads – $2,400
HiSeq High Output 2×100: 375k-425k clusters/mm2, 33-40 Gb data, 37.5 million reads – $2,400
Wednesday, January 15, 2014
Science enters $1,000 genome era
http://www.bbc.co.uk/news/science-environment-25751958
The ability to sequence a human genome for just $1,000 has arrived, a US genetic technology company has announced.
The HiSeq X Ten high throughput genetic sequencing machine was announced at the annual JP Morgan Healthcare Conference in San Francisco this week. The company said it had broken the "sound barrier" of human genomics.
The ability to sequence a human genome for just $1,000 has arrived, a US genetic technology company has announced.
The HiSeq X Ten high throughput genetic sequencing machine was announced at the annual JP Morgan Healthcare Conference in San Francisco this week. The company said it had broken the "sound barrier" of human genomics.
Friday, July 5, 2013
Mutational heterogeneity in cancer and the search for new cancer-associated genes
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12213.html
Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer1, 2, 3, 4, 5,6, 7, 8, 9. These studies involve the sequencing of matched tumour–normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour–normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.
Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer1, 2, 3, 4, 5,6, 7, 8, 9. These studies involve the sequencing of matched tumour–normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour–normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.
Wednesday, April 3, 2013
Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders
Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders
http://www.nature.com/jhg/journal/v57/n10/full/jhg201291a.html
Traditional approaches for gene mapping from candidate gene studies to positional cloning strategies have been applied for Mendelian disorders. Since 2005, next-generation sequencing (NGS) technologies are improving as rapid, high-throughput and cost-effective approaches to fulfill medical sciences and research demands. Using NGS, the underlying causative genes are directly distinguished via a systematic filtering, in which the identified gene variants are checked for novelty and functionality. During the past 2 years, the role of more than 100 genes has been distinguished in rare Mendelian disorders by means of whole-exome sequencing (WES). Combination of WES with traditional approaches, consistent with linkage analysis, has had the greatest impact on those disorders following autosomal mode of inheritance; in more than 60 identified genes, the causal variants have been transmitted at homozygous or compound heterozygous state. Recent literatures focusing on identified new causal genes in Mendelian disorders using WES are reviewed in the present survey.
Keywords: exome sequencing; mendelian disorder; mutation; next-generation sequencing; NGS; WES
A critical step in detecting variants from next-generation sequencing data ispost hoc filtering of putative variants called or predicted by computational tools. Here, we highlight four critical parameters that could enhance the accuracy of called single nucleotide variants and insertions/deletions: quality and deepness, refinement and improvement of initial mapping, allele/strand balance, and examination of spurious genes. Use of these sequence features appropriately in variant filtering could greatly improve validation rates, thereby saving time and costs in next-generation sequencing projects.
http://www.nature.com/jhg/journal/v57/n10/full/jhg201291a.html
Traditional approaches for gene mapping from candidate gene studies to positional cloning strategies have been applied for Mendelian disorders. Since 2005, next-generation sequencing (NGS) technologies are improving as rapid, high-throughput and cost-effective approaches to fulfill medical sciences and research demands. Using NGS, the underlying causative genes are directly distinguished via a systematic filtering, in which the identified gene variants are checked for novelty and functionality. During the past 2 years, the role of more than 100 genes has been distinguished in rare Mendelian disorders by means of whole-exome sequencing (WES). Combination of WES with traditional approaches, consistent with linkage analysis, has had the greatest impact on those disorders following autosomal mode of inheritance; in more than 60 identified genes, the causal variants have been transmitted at homozygous or compound heterozygous state. Recent literatures focusing on identified new causal genes in Mendelian disorders using WES are reviewed in the present survey.
Keywords: exome sequencing; mendelian disorder; mutation; next-generation sequencing; NGS; WES
Computational and statistical approaches to analyzing variants identified by exome sequencing
http://genomebiology.com/2011/12/9/227Consensus Rules in Variant Detection from Next-Generation Sequencing Data
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038470#s4A critical step in detecting variants from next-generation sequencing data ispost hoc filtering of putative variants called or predicted by computational tools. Here, we highlight four critical parameters that could enhance the accuracy of called single nucleotide variants and insertions/deletions: quality and deepness, refinement and improvement of initial mapping, allele/strand balance, and examination of spurious genes. Use of these sequence features appropriately in variant filtering could greatly improve validation rates, thereby saving time and costs in next-generation sequencing projects.
Wednesday, February 20, 2013
Friday, February 8, 2013
BGI
http://www.businessweek.com/articles/2013-02-07/bgis-young-chinese-scientists-will-map-any-genome
In agriculture, BGI is mapping genome sequences it considers proprietary and using them to engineer superior strains of rice, millet, and even fish.
The company changed its name from Beijing Genomics Institute to BGI Shenzhen and moved to the shoe factory.
In 2011, BGI reported revenue of 1.2 billion yuan. Many projects the company takes on reflect this policy of for-profit science.
BGI’s footprint is expanding. It recently received approval from the U.S. government to acquire its biggest competitor, Mountain View (Calif.)-based Complete Genomics (GNOM), which also provides commercial DNA sequencing
Complete Genomics will extend BGI’s reach, not only in terms of customers and sequencing power, but also in terms of data storage. Complete Genomics has established its own database of genetic information, complementing BGI’s efforts to build a cloud computing platform capable of holding large amounts of genomic data.
Companies that offer personalized genetic testing, such as 23andMe, typically test only for a sampling of 100 traits and diseases, or about 1/3,000th of the entire genome, Church says. For about $4,000, BGI does the whole thing.
“You’re looking for variants or parts of the genome that are hard to map,” he says. Computer programs have difficulty identifying a new variation unless a spot on the genome has already been pinpointed and entered into the computer program.
“It’s my belief that science has no limits.”
In agriculture, BGI is mapping genome sequences it considers proprietary and using them to engineer superior strains of rice, millet, and even fish.
The company changed its name from Beijing Genomics Institute to BGI Shenzhen and moved to the shoe factory.
In 2011, BGI reported revenue of 1.2 billion yuan. Many projects the company takes on reflect this policy of for-profit science.
BGI’s footprint is expanding. It recently received approval from the U.S. government to acquire its biggest competitor, Mountain View (Calif.)-based Complete Genomics (GNOM), which also provides commercial DNA sequencing
Complete Genomics will extend BGI’s reach, not only in terms of customers and sequencing power, but also in terms of data storage. Complete Genomics has established its own database of genetic information, complementing BGI’s efforts to build a cloud computing platform capable of holding large amounts of genomic data.
Companies that offer personalized genetic testing, such as 23andMe, typically test only for a sampling of 100 traits and diseases, or about 1/3,000th of the entire genome, Church says. For about $4,000, BGI does the whole thing.
“You’re looking for variants or parts of the genome that are hard to map,” he says. Computer programs have difficulty identifying a new variation unless a spot on the genome has already been pinpointed and entered into the computer program.
“It’s my belief that science has no limits.”
Friday, February 1, 2013
Genotype and SNP calling from next-generation sequencing data
http://www.nature.com/nrg/journal/v12/n6/pdf/nrg2986.pdf
Abstract
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies.
Abstract
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data. We review these methods and provide a guide for their use in NGS studies.
Wednesday, January 16, 2013
Disease gene identification by exome sequencing
http://www.genomics.agilent.com/GenericB.aspx?pagetype=Custom&subpagetype=Custom&pageid=3095
This presentation highlights the use of SureSelect Human All Exon kits for disease gene identification, with a focus on de novo mutations and clinical research applications - Alexander Hoischen Ph.D., Radboud University Nijmegen Medical Centre.
This presentation highlights the use of SureSelect Human All Exon kits for disease gene identification, with a focus on de novo mutations and clinical research applications - Alexander Hoischen Ph.D., Radboud University Nijmegen Medical Centre.
Tuesday, January 8, 2013
Translating genes into health
http://www.nature.com/ng/journal/v45/n1/full/ng.2510.html?WT.ec_id=NG-201301
A major challenge for genomics is to provide clinical benefits to the genetically diverse human population. Genome science has achieved a catalog of mutations and informative SNPs. Next-generation sequencing is rapidly delivering thousands of complete human genomes, but understanding and applying genomic knowledge remains a daunting undertaking. These challenges and opportunities for genomic medicine were central themes of the Golden Helix Symposium held in Turin, Italy, 18–21 April 2012.
A major challenge for genomics is to provide clinical benefits to the genetically diverse human population. Genome science has achieved a catalog of mutations and informative SNPs. Next-generation sequencing is rapidly delivering thousands of complete human genomes, but understanding and applying genomic knowledge remains a daunting undertaking. These challenges and opportunities for genomic medicine were central themes of the Golden Helix Symposium held in Turin, Italy, 18–21 April 2012.
The expanding scope of DNA sequencing
http://www.nature.com/nbt/journal/v30/n11/abs/nbt.2421.html
In just seven years, next-generation technologies have reduced the cost and increased the speed of DNA sequencing by four orders of magnitude, and experiments requiring many millions of sequencing reads are now routine. In research, sequencing is being applied not only to assemble genomes and to investigate the genetic basis of human disease, but also to explore myriad phenomena in organismic and cellular biology. In the clinic, the utility of sequence data is being intensively evaluated in diverse contexts, including reproductive medicine, oncology and infectious disease. A recurrent theme in the development of new sequencing applications is the creative 'recombination' of existing experimental building blocks. However, there remain many potentially high-impact applications of next-generation DNA sequencing that are not yet fully realized.
In just seven years, next-generation technologies have reduced the cost and increased the speed of DNA sequencing by four orders of magnitude, and experiments requiring many millions of sequencing reads are now routine. In research, sequencing is being applied not only to assemble genomes and to investigate the genetic basis of human disease, but also to explore myriad phenomena in organismic and cellular biology. In the clinic, the utility of sequence data is being intensively evaluated in diverse contexts, including reproductive medicine, oncology and infectious disease. A recurrent theme in the development of new sequencing applications is the creative 'recombination' of existing experimental building blocks. However, there remain many potentially high-impact applications of next-generation DNA sequencing that are not yet fully realized.
The battle for sequencing supremacy
http://www.nature.com/nbt/journal/v30/n11/full/nbt.2412.html
Today, the HiSeq 2000 instrument can generate up to 600 Gb of sequence data in about 10 days, sufficient to sequence four entire human genomes with each base sequenced an average of 30 times (30× depth of coverage). This throughput and quality also come with a high price tag (~$700,000 for the instrument and $6,000–8,000 per genome), but with over 1,000 instruments placed worldwide, the HiSeq 2000 is the backbone of most cutting-edge sequencing centers.
It also faces stiff competition from Illumina, whose benchtop MiSeq is more expensive upfront and slower, but also generates more data—more accurately, according to some studies. Both Ion Torrent and 454 sequencing tend to encounter problems with homopolymers, misreading stretches of sequence where the same nucleotide is repeated many times and generating inappropriate insertions or deletions (indels). “Based on our diligence, homopolymers continue to be an issue for Life Tech, and I think the MiSeq has a considerable lead in data accuracy,” says William Quirk, managing director and senior research analyst at PiperJaffray.
At present, though, most clinically minded companies see the greatest opportunity in developing assays for targeted resequencing of individual loci associated with disease—applications where small, high-speed benchtop instruments are ideal. “Life Technology recently announced that more than 50% of their PGM placements now are going into the clinic,” says Quirk. Some centers, like the Ontario Institute for Cancer Research, are already using tumor sequencing to guide patient treatment, and McPherson reports that instruments like the MiSeq have proven quite effective in enabling his team to act quickly and confidently. “We're trying to return results—from the time the patient is consented to the time the clinician gets a report—in three weeks,” he says. “That requires that the sequencing doesn't take more than a day or two.”
Illumina and Life Technologies have been quick to recognize this opportunity, and both MiSeq and PGM are undergoing US Food and Drug Administration (FDA) evaluation for general use as clinical instruments.
Targeted clinical diagnostics is also the primary focus of Cambridge, Massachusetts–based GnuBio, a startup that has largely stayed below the radar, but already has a working instrument installed at Canada's Montreal Heart Institute. In their system, a microfluidic workflow combines PCR amplicons from a genomic sample with nanodroplets containing one of ~5,000 different hexameric sequencing primers, each associated with a specific dye barcode.
Today, the HiSeq 2000 instrument can generate up to 600 Gb of sequence data in about 10 days, sufficient to sequence four entire human genomes with each base sequenced an average of 30 times (30× depth of coverage). This throughput and quality also come with a high price tag (~$700,000 for the instrument and $6,000–8,000 per genome), but with over 1,000 instruments placed worldwide, the HiSeq 2000 is the backbone of most cutting-edge sequencing centers.
It also faces stiff competition from Illumina, whose benchtop MiSeq is more expensive upfront and slower, but also generates more data—more accurately, according to some studies. Both Ion Torrent and 454 sequencing tend to encounter problems with homopolymers, misreading stretches of sequence where the same nucleotide is repeated many times and generating inappropriate insertions or deletions (indels). “Based on our diligence, homopolymers continue to be an issue for Life Tech, and I think the MiSeq has a considerable lead in data accuracy,” says William Quirk, managing director and senior research analyst at PiperJaffray.
At present, though, most clinically minded companies see the greatest opportunity in developing assays for targeted resequencing of individual loci associated with disease—applications where small, high-speed benchtop instruments are ideal. “Life Technology recently announced that more than 50% of their PGM placements now are going into the clinic,” says Quirk. Some centers, like the Ontario Institute for Cancer Research, are already using tumor sequencing to guide patient treatment, and McPherson reports that instruments like the MiSeq have proven quite effective in enabling his team to act quickly and confidently. “We're trying to return results—from the time the patient is consented to the time the clinician gets a report—in three weeks,” he says. “That requires that the sequencing doesn't take more than a day or two.”
Illumina and Life Technologies have been quick to recognize this opportunity, and both MiSeq and PGM are undergoing US Food and Drug Administration (FDA) evaluation for general use as clinical instruments.
Targeted clinical diagnostics is also the primary focus of Cambridge, Massachusetts–based GnuBio, a startup that has largely stayed below the radar, but already has a working instrument installed at Canada's Montreal Heart Institute. In their system, a microfluidic workflow combines PCR amplicons from a genomic sample with nanodroplets containing one of ~5,000 different hexameric sequencing primers, each associated with a specific dye barcode.
Monday, January 7, 2013
The New York Genome Center
http://www.nature.com/nbt/journal/v30/n11/full/nbt.2429.html
Nancy J. Kelley is founding executive director of the New York Genome Center (NYGC), an independent, nonprofit research organization whose mission is “to transform genomic research and healthcare for New York and the world”. Institutional founding members include Cold Spring Harbor Laboratory, Columbia University, Cornell University/Weill Cornell Medical College, The Jackson Laboratory, Memorial Sloan-Kettering Cancer Center, Mount Sinai Medical Center, NewYork-Presbyterian Hospital, New York University/NYU School of Medicine, North Shore-LIJ Health System, The Rockefeller University, and Stony Brook University. NYGC chose Illumina as its founding technology collaborator. Nature Biotechnologytalked to Kelley about NYGC's plan to become one of the largest genomics and bioinformatics facilities in North America.
Nancy J. Kelley is founding executive director of the New York Genome Center (NYGC), an independent, nonprofit research organization whose mission is “to transform genomic research and healthcare for New York and the world”. Institutional founding members include Cold Spring Harbor Laboratory, Columbia University, Cornell University/Weill Cornell Medical College, The Jackson Laboratory, Memorial Sloan-Kettering Cancer Center, Mount Sinai Medical Center, NewYork-Presbyterian Hospital, New York University/NYU School of Medicine, North Shore-LIJ Health System, The Rockefeller University, and Stony Brook University. NYGC chose Illumina as its founding technology collaborator. Nature Biotechnologytalked to Kelley about NYGC's plan to become one of the largest genomics and bioinformatics facilities in North America.
Wednesday, January 2, 2013
Thursday, December 20, 2012
Genetic Variation in an Individual Human Exome
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000160
There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's ‘exome,’ which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the ~12,500 variants that affect the protein coding portion of an individual's genome. We identified ~10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs) in this individual, of which ~15–20% are rare in the human population. We predict ~1,500 nsSNPs affect protein function and these tend be heterozygous, rare, or novel. Of the ~700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions of amino acids in the corresponding protein, rather than introducing frameshifts. Coding indels also occur frequently at the termini of genes, so even if an indel causes a frameshift, an alternative start or stop site in the gene can still be used to make a functional protein. In summary, we reduced the set of ~12,500 nonsilent coding variants by ~8-fold to a set of variants that are most likely to have major effects on their proteins' functions. This is our first glimpse of an individual's exome and a snapshot of the current state of personalized genomics. The majority of coding variants in this individual are common and appear to be functionally neutral. Our results also indicate that some variants can be used to improve the current NCBI human reference genome. As more genomes are sequenced, many rare variants and non-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformatic methods to hone in on possible functional variation.
There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized genomics. We focus here on the variants in a person's ‘exome,’ which is the set of exons in a genome, because the exome is believed to harbor much of the functional variation. We provide an analysis of the ~12,500 variants that affect the protein coding portion of an individual's genome. We identified ~10,400 nonsynonymous single nucleotide polymorphisms (nsSNPs) in this individual, of which ~15–20% are rare in the human population. We predict ~1,500 nsSNPs affect protein function and these tend be heterozygous, rare, or novel. Of the ~700 coding indels, approximately half tend to have lengths that are a multiple of three, which causes insertions/deletions of amino acids in the corresponding protein, rather than introducing frameshifts. Coding indels also occur frequently at the termini of genes, so even if an indel causes a frameshift, an alternative start or stop site in the gene can still be used to make a functional protein. In summary, we reduced the set of ~12,500 nonsilent coding variants by ~8-fold to a set of variants that are most likely to have major effects on their proteins' functions. This is our first glimpse of an individual's exome and a snapshot of the current state of personalized genomics. The majority of coding variants in this individual are common and appear to be functionally neutral. Our results also indicate that some variants can be used to improve the current NCBI human reference genome. As more genomes are sequenced, many rare variants and non-SNP variants will be discovered. We present an approach to analyze the coding variation in humans by proposing multiple bioinformatic methods to hone in on possible functional variation.
Difference between samtools and gatk algorithms
http://www.biostars.org/p/57149/
n general, samtools focuses more on a multi-purpose tool. It tends to use filters producing less bias. It produces the consensus in a more uniform (and the right) way and has the ability to infers population parameters not doable with GATK. I would say GATK focuses more on variant calling for human data. -- lh3
n general, samtools focuses more on a multi-purpose tool. It tends to use filters producing less bias. It produces the consensus in a more uniform (and the right) way and has the ability to infers population parameters not doable with GATK. I would say GATK focuses more on variant calling for human data. -- lh3
Thursday, November 29, 2012
Analysis of the bread wheat genome using whole-genome shotgun sequencing.
http://www.sciencedaily.com/releases/2012/11/121128143545.htm
Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary L. A. Barker, Rosalinda D’Amore, Alexandra M. Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser, Suzanne Kay, Darren Waite, Martin Trick, Ian Bancroft, Yong Gu, Naxin Huo, Ming-Cheng Luo, Sunish Sehgal, Bikram Gill, Sharyar Kianian, Olin Anderson, Paul Kersey, Jan Dvorak, W. Richard McCombie, Anthony Hall, Klaus F. X. Mayer, Keith J. Edwards, Michael W. Bevan, Neil Hall. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 2012; 491 (7426): 705 DOI: 10.1038/nature11650
The wheat genome is five times the size of the human genome, giving it a complexity that makes it difficult to study.
Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.
Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary L. A. Barker, Rosalinda D’Amore, Alexandra M. Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser, Suzanne Kay, Darren Waite, Martin Trick, Ian Bancroft, Yong Gu, Naxin Huo, Ming-Cheng Luo, Sunish Sehgal, Bikram Gill, Sharyar Kianian, Olin Anderson, Paul Kersey, Jan Dvorak, W. Richard McCombie, Anthony Hall, Klaus F. X. Mayer, Keith J. Edwards, Michael W. Bevan, Neil Hall. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 2012; 491 (7426): 705 DOI: 10.1038/nature11650
The wheat genome is five times the size of the human genome, giving it a complexity that makes it difficult to study.
Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.
Monday, September 17, 2012
Vancouver Prostate Centre Next-Gen Sequencing
slebihan@prostatecentre.com
Metagenomic research
Energy production, bioremediation
microbe, dentistry
marine biology
soil
for:
microbial and metabolic diversity
microbial abundance
gene content
metatranscriptomics
metabolic signature profiling
viral pathogen detection
16S/18S rRNA Amplicon Sequencing and Shotgun Sequencing
Metagenomic research
Energy production, bioremediation
microbe, dentistry
marine biology
soil
for:
microbial and metabolic diversity
microbial abundance
gene content
metatranscriptomics
metabolic signature profiling
viral pathogen detection
16S/18S rRNA Amplicon Sequencing and Shotgun Sequencing
Saturday, September 8, 2012
ENCODE
http://o.canada.com/2012/09/07/huge-dna-project-offers-guidebook-to-human-genome-200-m-encode-collaboration-releases-30-new-studies/
NEW YORK — In the largest single batch of discoveries about human DNA since the completion of the human genome project in 2003, 442 scientists in labs across three continents released 30 studies jam-packed with finds this week.
The discoveries, representing what the journal Nature calls the “guidebook to the human genome,” range from the esoteric — what is a gene? — to the practical — that just 20 gene switches may underlie 17 seemingly unrelated cancers, giving companies a workable number of drug targets.
The studies come from a $196-million project called the Encyclopedia of DNA Elements, or ENCODE, whose goal is to take the babel produced by the human genome project — the sequence of 3.2 billion chemical “bases” or “letters” that constitute the human genome — and make sense of it.
NEW YORK — In the largest single batch of discoveries about human DNA since the completion of the human genome project in 2003, 442 scientists in labs across three continents released 30 studies jam-packed with finds this week.
The discoveries, representing what the journal Nature calls the “guidebook to the human genome,” range from the esoteric — what is a gene? — to the practical — that just 20 gene switches may underlie 17 seemingly unrelated cancers, giving companies a workable number of drug targets.
The studies come from a $196-million project called the Encyclopedia of DNA Elements, or ENCODE, whose goal is to take the babel produced by the human genome project — the sequence of 3.2 billion chemical “bases” or “letters” that constitute the human genome — and make sense of it.
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