Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
Isidro Cortés‐CirianoJake June-Koo LeeRuibin XiDhawal JainYoungsook L. JungLixing YangDmitry A. GordeninLeszek J. KlimczakCheng‐Zhong ZhangDavid PellmanKadir C. AkdemirEva G. ÁlvarezAdrian Baez‐OrtegaRameen BeroukhimPaul C. BoutrosDavid D.L. BowtellBenedikt BrorsKathleen H. BurnsPeter J. CampbellKin ChanKen ChenIsidro Cortés‐CirianoAna Dueso-BarrosoAndrew DunfordPaul A. EdwardsXavier EstivillDariush EtemadmoghadamLars FeuerbachJ. Lynn FinkMilana Frenkel‐MorgensternDale W. GarsedMark GersteinDmitry A. GordeninDavid HaanJames E. HaberJulian M. HessBarbara HutterMarcin ImielińskiDavid JonesYoung Seok JuMarat D. KazanovYoungil KohJan O. KorbelKiran KumarEunjung Alice LeeYilong LiAndy G. LynchGeoff MacintyreFlorian MarkowetzIñigo MartincorenaAlexander Martinez‐FundichelySatoru MiyanoHidewaki NakagawaFábio C. P. NavarroStephan OssowskiJohn V. PearsonMontserrat PuiggròsKarsten RippeNicola D. RobertsSteven A. RobertsBernardo Rodríguez–MartínSteven E. SchumacherRalph ScullyMark ShackletonNikos SidiropoulosLina SieverlingChip StewartDavid TorrentsJosé M. C. TubíoIzar VillasanteNicola WaddellJeremiah A. WalaJoachim WeischenfeldtLixing YangXiaotong YaoSung-Soo YoonJorge ZamoraPeter J. ParkLauri A. AaltonenFederico AbascalAdam AbeshouseHiroyuki AburataniDavid J. AdamsNishant AgrawalKeun Soo AhnSung-Min AhnHiroshi AikataRehan AkbaniKadir C. AkdemirHikmat Al‐AhmadieSultan T. Al‐SedairyFátima Al‐ShahrourMalik AlawiMonique AlbertKenneth AldapeLudmil B. AlexandrovAdrian AllyKathryn AlsopEva G. ÁlvarezFernanda AmarySamirkumar B. AminBrice AminouOle AmmerpohlMatthew J. AndersonYeng AngDavide AntonelloPavana AnurSamuel AparícioElizabeth L. AppelbaumYasuhito AraiAxel AretzKoji ArihiroShun‐ichi AriizumiJoshua ArmeniaLaurent ArnouldL. SylviaYassen AssenovGurnit AtwalSietse AukemaJ. Todd AumanMiriam R. R. AurePhilip AwadallaMarta AymerichGary D. BaderAdrian Baez‐OrtegaMatthew H. BaileyPeter J. BaileyMiruna BalasundaramSaianand BaluPratiti BandopadhayayRosamonde E. BanksStefano BarbiAndrew P. BarbourJonathan BarenboimJill S. Barnholtz‐SloanHugh BarrElisabet BarreraJohn M.S. BartlettJavier BartoloméClaudio BassiOliver F. BatheDaniel BaumhoerPrashant BaviStephen B. BaylinWojciech BażantDuncan BeardsmoreTimothy A. BeckSam BehjatiAndreas BehrenBeifang NiuCindy BellSergi BeltránChristopher C. BenzAndrew BerchuckAnke K. BergmannErik N. BergstromBenjamin P. BermanDaniel M. BerneyStephan WolfRameen BeroukhimMario BerríosSamantha BersaniJohanna BertlMiguel BetancourtVinayak BhandariShriram G. BhosleAndrew V. BiankinMatthias BiegDarell D. BignerHans BinderEwan BirneyMichael J. BirrerNidhan K. BiswasBodil BjerkehagenTom BodenheimerLori BoiceGiada BonizzatoJohann S. de BonoArnoud BootArnoud BootÅke BorgArndt BorkhardtKeith A. BoroevichIvan BorozanChristoph W. BorstMarcus BosenbergMattia BosioJacqueline BoultwoodGuillaume BourquePaul C. BoutrosG. Steven BovaDavid BowenReanne BowlbyDavid D.L. BowtellSandrine BoyaultRich BoyceJeffrey M. BoydAlvis BrāzmaPaul BrennanDaniel BrewerArie B. BrinkmanRobert G. BristowRussell R. BroaddusJane E. BrockMalcolm V. BrockAnnegien BroeksAngela N. BrooksDenise BrooksBenedikt BrorsSøren BrunakTimothy J. C. BruxnerAlicia L. BruzosAlex BuchananIvo BuchhalterChristiane BuchholzSusan BullmanHazel BurkeBirgit BurkhardtKathleen H. BurnsJohn BusanovichCarlos D. BustamanteAdam P. ButlerAtul J. ButteNiall J. ByrneAnne‐Lise Børresen‐DaleRory JohnsonAndy CafferkeyDeclan CahillClaudia CalabreseCarlos CaldasFabien CalvoNiedzica CamachoPeter J. CampbellElı́as CampoCinzia CantùShaolong CaoThomas E. CareyJoana Carlevaro-FitaRebecca CarlsenIvana CataldoMario CazzolaJonathan CebonRobert CerfolioDianne ChadwickDimple ChakravartyDrc ChalmersCalvin Wing Yiu ChanKin ChanMichelle Chan‐Seng‐YueVishal S. ChandanDavid K. ChangStephen J. ChanockKeiran RaineAurélien ChateignerNilanjan ChatterjeeKazuaki ChayamaHsiao‐Wei ChenJieming ChenKen ChenYiwen ChenZhaohong ChenAndrew D. CherniackJeremy ChienYoke-Eng ChiewSuet‐Feung ChinJuok ChoSunghoon ChoJung Kyoon ChoiWan ChoiChristine ChomienneZechen ChongSu Pin ChooAngela ChouAngelika N. ChristElizabeth L. ChristieEric ChuahCarrie CibulskisKristian CibulskisSara CingarliniPeter ClaphamAlexander ClaviezSean P. ClearyNicole CloonanMarek CmeroColin C. CollinsAshton A. ConnorSusanna L. CookeColin S. CooperLeslie CopeVincenzo CorboMatthew G. CordesStephen CordnerIsidro Cortés‐CirianoKyle CovingtonPrue A. CowinBrian CraftDavid CraftChad J. CreightonYupeng CunErin CurleyIoana CutcutacheKarolina CzajkaBogdan CzerniakRebecca A. DaggLudmila DanilovaMaria Vittoria DavìNatalie R. DavidsonHelen DaviesIan J. DavisBrandi N. Davis‐DusenberyKevin J. DawsonFrancisco M. De La VegaRicardo De Paoli‐IseppiTimothy DefreitasAngelo Paolo Dei TosOlivier DelaneauJohn A. 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The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. Here, we developed a HUman Pan-genome ANalysis (HUPAN) system to build the human pan-genome. We applied it to 185 deep sequencing and 90 assembled Han Chinese genomes and detected 29.5 Mb novel genomic sequences and at least 188 novel protein-coding genes missing in the human reference genome (GRCh38). It can be an important resource for the human genome-related biomedical studies, such as cancer genome analysis. HUPAN is freely available at http://cgm.sjtu.edu.cn/hupan/ and https://github.com/SJTU-CGM/HUPAN .
Human genetics
Cancer genome sequencing
Personal genomics
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Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes are contaminated by human sequence. The contaminant sequences derive primarily from high-copy human repeat regions, which themselves are not adequately represented in the current human reference genome, GRCh38. The absence of the sequences from the human assembly offers a likely explanation for their presence in bacterial assemblies. In some cases, the contaminating contigs have been erroneously annotated as containing protein-coding sequences, which over time have propagated to create spurious protein “families” across multiple prokaryotic and eukaryotic genomes. As a result, 3437 spurious protein entries are currently present in the widely used nr and TrEMBL protein databases. We report here an extensive list of contaminant sequences in bacterial genome assemblies and the proteins associated with them. We found that nearly all contaminants occurred in small contigs in draft genomes, which suggests that filtering out small contigs from draft genome assemblies may mitigate the issue of contamination while still keeping nearly all of the genuine genomic sequences.
Bacterial genome size
RefSeq
Proteogenomics
Proteome
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The completion of the Human Genome Project in 2003 led to the launch of several major projects, including the international HapMap Project to identify genetic variants and haplotypes in the human genome (1), the 1000 Genomes Project to characterize the frequency of genetic variants in human populations (2), the ENCODE project to identify functional elements in the human genome (3,4), and the ROADMAP project to assess epigenetic alternation of DNA sequences (5). All these projects have yielded unprecedented information on the human genome: for instance, exon regions of genes are seen to make up less than 2% of the human genome. Most of the human genome (98%) is thus non-coding but contains many regulatory elements, including enhancers, silencers, insulators, or locus control regions (LCR).
International HapMap Project
ENCODE
Cancer genome sequencing
1000 Genomes Project
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This chapter contains sections titled: Summary of the Chapter Definitions of Keywords Introduction. Short History of the Human Genome Project Vectors. Description of the Main Types of Vectors Used in the HGP Mapping of the Human Genome Main Approaches to Sequence Human Genome Identification of Genes. How Many Genes Are in the Human Genome? Was it Worth to it Sequence Human Genome? Acknowledgment References
ENCODE
Identification
Sequence (biology)
Cancer genome sequencing
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