Abstract
Next-generation sequencing (NGS) technologies have revolutionized the field of genomics and provided unprecedented opportunities for high-throughput analysis at the levels of genomics, transcriptomics and epigenetics. However, the cost of NGS is still prohibitive for many laboratories. It is imperative to address the trade-off between the sequencing depth and cost. In this review, we will discuss the effects of sequencing depth on the detection of genes, quantification of gene expression and discovering of gene structural variants. This will provide readers information on choosing appropriate sequencing depth that best meet the needs of their particular project.
Article PDF
Similar content being viewed by others
References
Sanger F, Nicklen S, Coulson A R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA, 1977, 74: 5463–5467
Metzker M L. Sequencing technologies—the next generation. Nat Rev Genet, 2010, 11: 31–46
Huang S, Li R, Zhang Z, et al. The genome of the cucumber, Cucumis sativus L. Nat Genet, 2009, 41: 1275–1281
Li R, Fan W, Tian G, et al. The sequence and de novo assembly of the giant panda genome. Nature, 2010, 463: 311–317
Hernandez D, Francois P, Farinelli L, et al. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res, 2008, 18: 802–809
Wheeler D A, Srinivasan M, Egholm M, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature, 2008, 452: 872–876
van Tassell C P, Smith T P, Matukumalli L K, et al. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods, 2008, 5: 247–252
Baird N A, Etter P D, Atwood T S, et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 2008, 3: e3376
Wang S, Meyer E, McKay J K, et al. 2b-RAD: a simple and flexible method for genome-wide genotyping. Nat Methods, 2012, 9: 808–810
Ng S B, Turner E H, Robertson P D, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 2009, 461: 272–276
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet, 2009, 10: 57–63
Fodor S P, Rava R P, Huang X C, et al. Multiplexed biochemical assays with biological chips. Nature, 1993, 364: 555–556
Morin R D, O’Connor M D, Griffith M, et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res, 2008, 18: 610–621
Lister R, O’Malley R C, Tonti-Filippini J, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 2008, 133: 523–536
Ordway J M, Budiman M A, Korshunova Y, et al. Identification of novel high-frequency DNA methylation changes in breast cancer. PLoS ONE, 2007, 2: e1314
Johnson D S, Mortazavi A, Myers R M, et al. Genome-wide mapping of in vivo protein-DNA interactions. Science, 2007, 316: 1497–1502
Huang Q, Lin B, Liu H, et al. RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma. PLoS ONE, 2011, 6: e26168
Toung J M, Morley M, Li M, et al. RNA-sequence analysis of human B-cells. Genome Res, 2011, 21: 991–998
Tarazona S, Garcia-Alcalde F, Dopazo J, et al. Differential expression in RNA-seq: a matter of depth. Genome Res, 2011, 21: 2213–2223
Mortazavi A, Williams B A, McCue K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods, 2008, 5: 621–628
Xu W, Seok J, Mindrinos M N, et al. Human transcriptome array for high-throughput clinical studies. Proc Natl Acad Sci USA, 2011, 108: 3707–3712
Pan Q, Shai O, Lee L J, et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet, 2008, 40: 1413–1415
Cirulli E T, Singh A, Shianna K V, et al. Screening the human exome: a comparison of whole genome and whole transcriptome sequencing. Genome Biol, 2010, 11: R57
Ng S B, Buckingham K J, Lee C, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet, 2010, 42: 30–35
Hoischen A, van Bon B W, Gilissen C, et al. De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet, 2010, 42: 483–485
Wang K, Kan J, Yuen S T, et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat Genet, 2011, 43: 1219–1223
Wei X, Walia V, Lin J C, et al. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet, 2011, 43: 442–446
Comino-Mendez I, Gracia-Aznarez F J, Schiavi F, et al. Exome sequencing identifies MAX mutations as a cause of hereditary pheochromocytoma. Nat Genet, 2011, 43: 663–667
Albers C A, Cvejic A, Favier R, et al. Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome. Nat Genet, 2011, 43: 735–737
Li M, Zhao H, Zhang X, et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat Genet, 2011, 43: 828–829
Xu B, Roos J L, Dexheimer P, et al. Exome sequencing supports a de novo mutational paradigm for schizophrenia. Nat Genet, 2011, 43: 864–868
Sloan J L, Johnston J J, Manoli I, et al. Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria. Nat Genet, 2011, 43: 883–886
Quesada V, Conde L, Villamor N, et al. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet, 2011, 44: 47–52
Nikolaev S I, Rimoldi D, Iseli C, et al. Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Genet, 2011, 44: 133–139
Ong C K, Subimerb C, Pairojkul C, et al. Exome sequencing of liver fluke-associated cholangiocarcinoma. Nat Genet, 2012, 44: 690–693
Arboleda V A, Lee H, Parnaik R, et al. Mutations in the PCNA-binding domain of CDKN1C cause IMAGe syndrome. Nat Genet, 2012, 44: 788–792
Barbieri C E, Baca S C, Lawrence M S, et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet, 44: 685–689
Wortmann S B, Vaz F M, Gardeitchik T, et al. Mutations in the phospholipid remodeling gene SERAC1 impair mitochondrial function and intracellular cholesterol trafficking and cause dystonia and deafness. Nat Genet, 2012, 44: 797–802
Lee J H, Huynh M, Silhavy J L, et al. De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly. Nat Genet, 2012, 44: 941–945
Heinzen E L, Swoboda K J, Hitomi Y, et al. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood. Nat Genet, 2012, 44: 1030–1034
Falk M J, Zhang Q, Nakamaru-Ogiso E, et al. NMNAT1 mutations cause Leber congenital amaurosis. Nat Genet, 2012, 44: 1040–1045
Harakalova M, van Harssel J J, Terhal P A, et al. Dominant missense mutations in ABCC9 cause Cantu syndrome. Nat Genet, 2012, 44: 793–796
Emond M J, Louie T, Emerson J, et al. Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Nat Genet, 2012, 44: 886–889
Hodis E, Watson I R, Kryukov G V, et al. A landscape of driver mutations in melanoma. Cell, 2012, 150: 251–263
Krauthammer M, Kong Y, Ha B H, et al. Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat Genet, 2012, 44: 1006–1014
Rademakers R, Baker M, Nicholson A M, et al. Mutations in the colony stimulating factor 1 receptor (CSF1R) gene cause hereditary diffuse leukoencephalopathy with spheroids. Nat Genet, 2012, 44: 200–205
Huang J, Deng Q, Wang Q, et al. Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat Genet, 2012, 44: 1117–1121
Peifer M, Fernandez-Cuesta L, Sos M L, et al. Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet, 2012, 44: 1104–1110
Rudin C M, Durinck S, Stawiski E W, et al. Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet, 2012, 44: 1111–1116
Rice G I, Kasher P R, Forte G M, et al. Mutations in ADAR1 cause Aicardi-Goutieres syndrome associated with a type I interferon signature. Nat Genet, 2012, 44: 1243–1248
Doyle A J, Doyle J J, Bessling S L, et al. Mutations in the TGF-beta repressor SKI cause Shprintzen-Goldberg syndrome with aortic aneurysm. Nat Genet, 2012, 44: 1249–1254
Barcia G, Fleming M R, Deligniere A, et al. De novo gain-of-function KCNT1 channel mutations cause malignant migrating partial seizures of infancy. Nat Genet, 2012, 44: 1255–1259
Bainbridge M N, Wang M, Burgess D L, et al. Whole exome capture in solution with 3 Gbp of data. Genome Biol, 2010, 11: R62
Clark M J, Chen R, Lam H Y, et al. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol, 2011, 29: 908–914
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
About this article
Cite this article
Hou, R., Yang, Z., Li, M. et al. Impact of the next-generation sequencing data depth on various biological result inferences. Sci. China Life Sci. 56, 104–109 (2013). https://doi.org/10.1007/s11427-013-4441-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11427-013-4441-0