The impact of next-generation sequencing on genomics

“Following completion of the HGP, a new approach, genome-wide association study (GWAS), was widely applied to genomics.”

“The core philosophy of massive parallel sequencing used in next-generation sequencing (NGS) is adapted from shotgun sequencing (Venter et al., 2003; Margulies et al., 2005; Shendure et al., 2005).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”

“Individual human genomes (one Asian and one African) have been successfully sequenced and assembled using the Illumina Genome Analyzer (read lengths ranged from 35 to 75 basepairs) with a modified SOAP program, SOAPdenovo (Li et al., 2010).”

“Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”

“Nano-technologies have long been considered a cutting-edge technology for single-molecule DNA sequencing (Iqbal et al., 2007; Branton et al., 2008) and several nanopore sequencing concepts and technologies are currently under development.”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“SIFT (Sorting Intolerant From Tolerant) is used to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of the amino acid can be applied to find non-synonymous polymorphisms within NGS data (Ng and Henikoff, 2001,2002).”

“Polymorphism Phenotyping (PolyPhen) and updated PolyPhen-2 are tools which predict the possible impact of an amino acid substitution on the structure and function of a specific protein using straightforward comparative physical methods (Sunyaev et al., 2001;Ramensky et al., 2002).”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“…strategy, the mutations in DHODH from four individuals from three unrelated families with Miller syndrome have been successfully identified (Ng et al., 2010a), illustrating that selective DNA enrichment techniques will dramatically reduce overall cost and accelerate discovery of genetic…”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“Shortly thereafter, the second complete individual genome (James D. Watson) was sequenced using next-generation technology, which marked the first human genome sequenced with new NGS technology (Wheeler et al., 2008).”

“Sanger sequencing was used to obtain the first consensus sequence of the human genome in 2001 (Lander et al., 2001; Venter et al., 2001) and the first individual human diploid sequence (J. Craig Venter) in 2007 (Levy et al., 2007).”

“Sanger sequencing was used to obtain the first consensus sequence of the human genome in 2001 (Lander et al., 2001; Venter et al., 2001) and the first individual human diploid sequence (J. Craig Venter) in 2007 (Levy et al., 2007).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“The core philosophy of massive parallel sequencing used in next-generation sequencing (NGS) is adapted from shotgun sequencing (Venter et al., 2003; Margulies et al., 2005; Shendure et al., 2005).”

“…strategy, the mutations in DHODH from four individuals from three unrelated families with Miller syndrome have been successfully identified (Ng et al., 2010a), illustrating that selective DNA enrichment techniques will dramatically reduce overall cost and accelerate discovery of genetic…”

“Such rare variants may have a large effect as genetic risk factors for complex genetic diseases (Frazer et al., 2009; Manolio et al., 2009; Schork et al., 2009; Tsuji, 2010).”

“Polymorphism Phenotyping (PolyPhen) and updated PolyPhen-2 are tools which predict the possible impact of an amino acid substitution on the structure and function of a specific protein using straightforward comparative physical methods (Sunyaev et al., 2001;Ramensky et al., 2002).”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“Predictor of human Deleterious Single Nucleotide Polymorphisms (PhD-SNP) is an optimized program to predict if a given single point protein mutation can be classified as disease-related or as neutral polymorphism based on protein sequence and profile information (Capriotti et al., 2006).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“It is a challenge to efficiently align short reads to a reference genome, especially when developing new algorithms to handle ambiguities or lack of accuracy during the alignment (Li and Homer, 2010).”

“Currently de novo assembly with NGS data is generally limited to microbial genome projects (Metagenomics) due to the small bacterial genome size (Chistoserdova, 2010; Wooley et al., 2010).”

“SIFT (Sorting Intolerant From Tolerant) is used to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of the amino acid can be applied to find non-synonymous polymorphisms within NGS data (Ng and Henikoff, 2001,2002).”

“Following completion of the HGP, a new approach, genome-wide association study (GWAS), was widely applied to genomics.”

“CloudBurst is another new parallel read-mapping cloud algorithm optimized for mapping NGS data to a human reference genome, SNP discovery, genotyping and personal genomics (Schatz, 2009).”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“…detection software, which includes screening genomes for structural and single nucleotide variants and the differences between genomes (Li et al., 2009; Medvedev et al., 2009; Thusberg and Vihinen, 2009), are generally integrated with alignment and assembly processes and are listed in Table 4.”

“The full benefit of NGS will not be achieved until bioinformatics are able to maximally interpret and utilize these short-read sequences, including alignment, assembly, etc (Pop and Salzberg, 2008).”

“Other genetic loci for rare diseases have also been successfully identified through exome sequencing (Bilguvar et al., 2010; Ng et al., 2010a,b; Rios et al., 2010; Walsh et al., 2010), further validating this strategy.”

“CrossBow is the first cloud computing software capable of performing alignment and single nucleotide polymorphism analysis on multiple whole-human datasets (Langmead et al., 2009).”

“Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”

“As such, advanced single DNA molecule sequencing technology has been defined as the next-NGS technology (Pettersson et al., 2009).”

“Nano-technologies have long been considered a cutting-edge technology for single-molecule DNA sequencing (Iqbal et al., 2007; Branton et al., 2008) and several nanopore sequencing concepts and technologies are currently under development.”

“By considering the physiochemical variations presented in protein sequence alignment and the property of variations, Multivariate Analysis of Protein Polymorphism (MAPP) can predict the impact of all possible amino acid substitutions on the function of the protein (Stone and Sidow, 2005).”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“Targeted sequencing generally focuses on all protein-coding subsequences (the functional exome), which only requires ~5% as much sequencing compared to that required for the entire human genome (Pussegoda, 2010; Senapathy et al., 2010; Teer and Mullikin, 2010).”

“Other genetic loci for rare diseases have also been successfully identified through exome sequencing (Bilguvar et al., 2010; Ng et al., 2010a,b; Rios et al., 2010; Walsh et al., 2010), further validating this strategy.”

“The primary goal of current algorithms and computing for short-read assembly with NGS technologies is to increase read length (Chaisson et al., 2009).”

“A common strategy for NGS is to use DNA synthesis or ligation process to read through many different DNA templates in parallel (Fuller et al., 2009).”

“Although several early GWAS studies reported potentially promising results, the majority of GWAS studies were disappointing because of inadequate sample size, limitation of arrays for certain genetic variations, and/or heterogeneity in phenotype (Daly, 2010a).”

“There is no doubt that the progress of genomics will eventually lead to the birth of genetic medicine which will propel significant advances and improvements in human health (Gonzalez-Angulo et al., 2010).”

“The parallel short-read strategy of NGS opens many challenges for bioinformatics to interpret the short reads and the genetic variations in human genomes (Wold and Myers, 2008; Yang et al., 2009).”

“…detection software, which includes screening genomes for structural and single nucleotide variants and the differences between genomes (Li et al., 2009; Medvedev et al., 2009; Thusberg and Vihinen, 2009), are generally integrated with alignment and assembly processes and are listed in Table 4.”

“Several unique single-molecule DNA sequencing technologies are currently under development; however, little information has been made publically available (Gupta, 2008; Xu et al., 2009; Metzker, 2010; Treffer and Deckert, 2010).”

“…selective DNA enrichment techniques improve the overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform coverage, high reproducibility, and…”

“By targeting specific regions of interest, selective DNA enrichment techniques improve the overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform…”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“…1000 genome project the cost of sequencing an individual genome has been rapidly decreasing and will likely reach $1000 per person within a short period of time (von Bubnoff, 2008), making personalized medicine become a possible reality (Lunshof et al., 2010; Mardis, 2006; Harismendy et al., 2009).”

“Other genetic loci for rare diseases have also been successfully identified through exome sequencing (Bilguvar et al., 2010; Ng et al., 2010a,b; Rios et al., 2010; Walsh et al., 2010), further validating this strategy.”

“At 600 bp, the 454 Sequencer has the longest short reads among all the NGS platforms; and generates ~400–600 Mb of sequence reads per run; critical for some applications such as RNA isoform identification in RNA-seq and de novo assembly of microbes in metagenomics (Mocali and Benedetti, 2010).”

“By targeting specific regions of interest, selective DNA enrichment techniques improve the overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform…”

“Efforts to date have focused on overcoming the limitation of short reads for genome-wide analysis, but unfortunately, current available bioinformatics ability and computing power is lagging far behind the needs for NGS sequencing data analysis (McPherson, 2009).”

“Some online utility programs, such as EagleView (Huang and Marth, 2008) or LookSeq (Manske and Kwiatkowski, 2009), also provide some additional assistance on NGS data analysis and interpretation (Table 3).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“Several unique single-molecule DNA sequencing technologies are currently under development; however, little information has been made publically available (Gupta, 2008; Xu et al., 2009; Metzker, 2010; Treffer and Deckert, 2010).”

“Although several early GWAS studies reported potentially promising results, the majority of GWAS studies were disappointing because of inadequate sample size, limitation of arrays for certain genetic variations, and/or heterogeneity in phenotype (Daly, 2010a).”

“In genomics, the personal genome era made available by NGS technologies will mark a significant milestone in entire genomic research field in the foreseeable future (Zhang and Dolan, 2010; Holmes et al., 2009).”

“Currently de novo assembly with NGS data is generally limited to microbial genome projects (Metagenomics) due to the small bacterial genome size (Chistoserdova, 2010; Wooley et al., 2010).”

“…1000 genome project the cost of sequencing an individual genome has been rapidly decreasing and will likely reach $1000 per person within a short period of time (von Bubnoff, 2008), making personalized medicine become a possible reality (Lunshof et al., 2010; Mardis, 2006; Harismendy et al., 2009).”

“…of heritability, indicating that GWAS based on the “common disease-common variants hypothesis” is not very effective in identifying genetic variants for complex traits, and common genetic variability is unlikely to explain the entire genetic predisposition to disease (Singleton et al., 2010).”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“Such rare variants may have a large effect as genetic risk factors for complex genetic diseases (Frazer et al., 2009; Manolio et al., 2009; Schork et al., 2009; Tsuji, 2010).”

“…overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform coverage, high reproducibility, and no allele bias for any genomic region (Stratton, 2008).”

“Several unique single-molecule DNA sequencing technologies are currently under development; however, little information has been made publically available (Gupta, 2008; Xu et al., 2009; Metzker, 2010; Treffer and Deckert, 2010).”

“Some online utility programs, such as EagleView (Huang and Marth, 2008) or LookSeq (Manske and Kwiatkowski, 2009), also provide some additional assistance on NGS data analysis and interpretation (Table 3).”

“…regions of interest, selective DNA enrichment techniques improve the overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform coverage, high…”

“The core philosophy of massive parallel sequencing used in next-generation sequencing (NGS) is adapted from shotgun sequencing (Venter et al., 2003; Margulies et al., 2005; Shendure et al., 2005).”

“The parallel short-read strategy of NGS opens many challenges for bioinformatics to interpret the short reads and the genetic variations in human genomes (Wold and Myers, 2008; Yang et al., 2009).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“The term “genomics” was used as the name of the first journal in the field of genomics (McKusick and Ruddle, 1987).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“In genomics, the personal genome era made available by NGS technologies will mark a significant milestone in entire genomic research field in the foreseeable future (Zhang and Dolan, 2010; Holmes et al., 2009).”

“It is challenging to develop software with the ability to distinguish low-frequency alleles descendent from ancient ancestors from de novo or extremely rare mutations recently introduced into the population (Nakken et al., 2007; van Oeveren and Janssen, 2009).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“It is challenging to develop software with the ability to distinguish low-frequency alleles descendent from ancient ancestors from de novo or extremely rare mutations recently introduced into the population (Nakken et al., 2007; van Oeveren and Janssen, 2009).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“New genomic technologies have revolutionized our understanding of many genes or genomic regions involved in the pathogenesis of human diseases (Novelli et al., 2010).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“Targeted sequencing generally focuses on all protein-coding subsequences (the functional exome), which only requires ~5% as much sequencing compared to that required for the entire human genome (Pussegoda, 2010; Senapathy et al., 2010; Teer and Mullikin, 2010).”

“Targeted sequencing generally focuses on all protein-coding subsequences (the functional exome), which only requires ~5% as much sequencing compared to that required for the entire human genome (Pussegoda, 2010; Senapathy et al., 2010; Teer and Mullikin, 2010).”

“Although available NGS technologies utilize quite diverse chemistry and base incorporation ⁄ detection tools, they share two main steps: library fragmentation ⁄ amplicon library preparation and detection of the incorporated nucleotides (Glenn 2011; Zhang et al. 2011).”

“Since the size of the data samples is constantly increasing [2, 3], Reactome offers a set of pathway analysis tools which aim to deal with this scenario and yet provide reliable and accurate results with interactive (seconds) response time for genome-wide datasets.”