Council on Dairy Cattle Breeding Navigation guide for Nominators · the “out” directory after...
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1| Page Council on Dairy Cattle Breeding Navigation guide for Nominators Latest update: October 24 th , 2017
Transcript of Council on Dairy Cattle Breeding Navigation guide for Nominators · the “out” directory after...
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CouncilonDairyCattleBreeding
NavigationguideforNominators
Latestupdate:October24th,2017
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Contents
1.DataFlowandExchange.........................................................................................................................4
1.1ReportCards.........................................................................................................................4
1.2DynamicsofDataFlow.........................................................................................................5
1.3DataFlowbetweenNominatorsandCDCB..........................................................................6
1.4StepstoReceiveEvaluationResultsfromCDCB...................................................................7
1.5DataExchangethroughsecureFTP......................................................................................82.FeeCodeinformation.............................................................................................................................9
2.1HowCDCBCollectsFeesthroughGenomicNominators......................................................9
3.Nomination...........................................................................................................................................10
3.1Nominationinformation.....................................................................................................10
3.2.NominationThroughWebQuery.......................................................................................10
3.3.NominationThroughsecureFTP(SFTP)............................................................................12
3.3.Format1andFormat1G...................................................................................................134.CommonReasonsfornotreceivinganEvaluation(andHowtoCorrecterrors)................................15
4.1WheretoFindGenomicConflicts.......................................................................................15
4.2Commonreasonsfornotreceivinganevaluation..............................................................16Genotypewasnotusableduetoaconflict,lowcallrate,beingacrossbred(PI=“B”)......................16
Thegenotypebecameusableafterthegenotypeswereextractedfortheevaluation....................16
Thebreedofevaluationisnotamongthosewegenerateevaluationsfor.......................................17
Theanimal’sgenotypeconflicteditsimputeddam...........................................................................18
Thefeecodeis“N(Nofeepaid)”or“H(Historic)”............................................................................18
Thebullhassemenmarketedandit’snotatriannualevaluationrelease........................................18
TheownerofthebullisnotlocatedintheUSandAIservicefeehasnotbeenpaid,sotheevaluationisnotpublic......................................................................................................................18
Thegenotypeisdesignatedparentageverificationonly(PI=“P”).....................................................19
Thebullisforeign,over15monthsofageandnoAIservicefeehasbeenpaid................................19
WronganimalID................................................................................................................................19
5.WebQueries..........................................................................................................................................20
5.1WhatisWebQueryandwhatcanwedowithit.........................................................................20
5.2CDCB-Nomination_Q...................................................................................................................20
5.3Affiliatespecificgenotypereports...............................................................................................20
5.4CheckFMT1records....................................................................................................................22
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5.5CheckDam...................................................................................................................................22
5.6Get116parentageSNPforalistofanimalIDs............................................................................24
5.7NewGenotypeQuery..................................................................................................................24
5.8GTFee..........................................................................................................................................25
5.9parentage.cfm..............................................................................................................................25
5.10GenotypeMove/SwapAPP........................................................................................................25
5.11getfee.........................................................................................................................................26
6. GenomicNominatorChecklist...........................................................................................................27
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1.DataFlowandExchange
1.1 Report Cards ReportCardsaremadeavailabletogenomicnominatorsonamonthlybasis.Theyprovidesummarystatisticsfromthegenotypessubmittedbyeachgenomicnominator.Sincethedataavailableinthedifferentsituationsisdifferent,notallmetricsareconsideredstrictly(herdswithregisteredcattleusuallyhavemoreaccuratepedigreedatathannon-registeredherdswithcommercialorientation).
1. Totalgenotypes.Determinedbymonthlyreleasedates.2. Numberofgenotypesforeachchiptype.3. Genotypesmissingnominationwhenloaded.Nominatorsarerequiredtosubmita
nominationforeachanimalbeforethegenotypeissubmittedtotheCDCBcollaboratordatabase,asstatedintheQualityCertificationRequirementsforGenomicNominators(https://redmine.uscdcb.com/documents/8).
4. GenotypeswithunknownanimalID(Identification).Thisoccurswhentheanimalhasnotbeennominatedandthegenotypesubmission:i)doesnotcontainanimalIDinformation,or;ii)theanimalIDhasnotbeenenteredintheCDCBcollaboratordatabase.
5. Sirespedigreemissing.FrequencyofmissingsireIDinformationintheCDCBdatabase.Commonreasonsare:thesireIDprovidedisinvalid,aherdbullisnotenrolledwithabreedassociation,oraforeignbull’spedigreehasnotbeenprovided.It’snominatorresponsibilitytoprovidethisinformation.
6. Dampedigreemissing.FrequencyofmissingdamIDinformationintheCDCBdatabase.7. Damblankedduetoconflict.DamIDwasprovidedbuttheinformationwasnotstoreddue
toaconflict.Commonreasonsare:theanimal’sbirthdatedidnotagreewiththedam’scalvingdate,amaternalsiblinghasabirthdatewithin9monthsoftheanimalsubmitted,etc.Thesechecksarebypassedforanimalscodedashavingresultedfromanembryotransferbirth.
8. IDswith573/574.NumericIDsstartingwiththesedigitsareassignedbythenominatorandtypicallynotattachedtotheanimal.Thepreferredsolutionistoidentifytheanimalbyatagattachedtotheanimal.
9. Groupnamenotfoundinfeetableforcodes1or2.TheDHIherdcodesuppliedwasnotfoundamongtheherdcodesthathaveafeecodeassigned.Thiscanbeexpectedtooccurforthoseherdsthathavebeguntestingrecently.
10. Groupnamenotfoundasaherdoftheanimalordam.TheherdcodeassignedbythenominatordoesnotagreewiththeoneintheCDCBcollaboratordatabase,whichcamethroughDHI.
11. Genotypesnotusableduetoconflicts.Genomicconflictsareresultsofincorrectdata,suchasincorrectpedigree,identification,breedcode,sexetc.Thereforethisfrequencyofthegenomicconflictinverselyrelatedtoaccuracyofsubmission.
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12. Genotypeswithfeecode=NAcompletenominationrequiresassignmentoffeecode,thereforenonominationshouldbeleftwithfeecode=N.
13. GenotypeswithassignmenttoanimalchangedAgenotypereassignmentindicatesincorrectindicationofpedigree/nomination.Thisreportshowsnumberofgenotypesthatwerereassignedduringthemonth.
14. AnimalswithachangeinsireordamChangingasire/damindicatesincorrectpedigree.Itisnominator’sresponsibilitytoensurecorrectpedigree.
Exampleofareportcard:
1000,TotalgenotypesforNOMINATORXforYYMM
130,CHIP1
870,CHIP2
4,Genotypesmissingnominationwhenloaded
1,GenotypeswithunknownanimalID
5,Sirepedigreemissing
926,Dampedigreemissing
22,Damblankedduetoconflict
5,IDswith573/574
12,Group_Namenotfoundinfeetableforfeecodes1or2
9,Group_Namenotfoundasaherdofanimalordam
16,Genotypesnotusableduetoconflicts
22,Genotypeswithfeecode=N
13,Genotypeswithassignmenttoanimalchanged
84,Animalswithachangeinsireordam
1.2 Dynamics of Data Flow Thereare5categoriesoforganizationsthatinteractwiththeCDCBcollaboratordatabase:PurebreedDariyCattleAssociations(PDCA),DairyRecordsProcessingCenters(DRPC),DairyRecordProviders(DRP),NationalAssociationofAnimalBreeders(NAAB)andseveralinternationalpartners.Onceeachorganizationsubmitstheirdata,itisfirstqualitycheckedandgoodrecordsareloadedintotheCDCBcollaboratordatabase.ThedataisthenusedtoobtainandprovideaplethoraofCDCBservices,includinggeneticandgenomicevaluations.Thediagrambelowsummarizesthedataflow:
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1.3 Data Flow between Nominators and CDCB ThefollowingdiagramdescribesspecificallytheroleofGenomicNominatorsindataexchangeswiththeCDCBcollaboratordatabase.
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Theprocessstartswiththedecisionofadairyproduceroracompany(e.g.astud)toobtainagenomicevaluationfromCDCB.TheGenomicNominatorhasakeyroleintransformingthisdecisionintoanactualservice.ItmanagesthecollectionofbiologicalsamplesandensurestheyaresenttooneoftheCDCBcertifiedlaboratorieswiththecompleteandcorrectinformation.ItnominatestheanimalbeforethegenotypearrivesatCDCB.Itisimportanttostressthis:GenomicNominatorsarerequiredtocompletethenominationprocessbeforeCDCBreceivesthegenotype,asthepedigreeisanessentialpartoftheQCprocessofthegenotype.Nominationcanbedonethroughawebapplication(https://queries.uscdcb.com/CF-queries/Nom2.cfm-PASSWORDPROTECTED)orbysubmittingformat1GtotheGenomicNominator“in”directoryintheCDCBsftparea.
Oncebothnominationandgenotypesubmissionstepsaresuccessfullycompletedandallconflicts/errorshavebeeneventuallycorrected,thegenomicnominatorwillreceiveafirstnon-officialweeklyevaluationandmonthlyofficialevaluationresults.Aslistedinthe“CorerequirementsforGenomicNominators”intheQualityCertificationRequirementsforGenomicNominators(https://redmine.uscdcb.com/documents/8),thenominatorisexpectedtodelivertheresultstotheherd/studoriginallyrequestingCDCBservices.
1.4 Steps to Receive Evaluation Results from CDCB 1. ThegenomicnominatorcollaborateswithaproducerandaCDCBapprovedGenotyping
Laboratorytoarrangethebiologicalsamplecollectionandsubmissiontothelab.TheGenomicNominatorisresponsiblethatallinformationcorrelatedwiththesampleisaccurateandcomplete.
2. BeforethesamplesaregenotypedandsubmittedtotheCDCBcollaboratordatabase,thegenomicnominatorisexpectedtocompletethenominationprocess.Nominationscanbecompletedonawebqueryorinbatch(i.e.multiplenominationsdonecontemporarily),throughthesubmissionofaformat1G(https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/Format_1)tothe“in”folderoftheCDCBSFTParea(ftp.uscdcb.com).Inthislattercase,typicallya“notify”fileisgeneratedinthe“out”directory.Thenominatorisexpectedtocheckthisfile:itcontainstheoutcomeofthenominationandlinkedinformation.
3. AfterthegenotypeisloadedintotheCDCBcollaboratordatabase,genotypeswitherrorsarereportedbackinthe“out”folderoftheCDCBsftparea.The“genomicerror”filecontainsalargenumberofinformationthatthegenomicnominatorshouldusetocorrecttheerrors.Onlygenotypesflaggedas“usable”withcompletenomination(andfeecodeassigned)qualifytoreceiveCDCBevaluations.
4. Newindividualswillobtainanon-officialweeklyevaluation(releasedonthenextTuesdayinthe“out”directoryafterthegenotypebecameusable).Theseanimalswillreceiveofficialmonthlyevaluationseverymonthaslongastheirgenotypeisflaggedas“usable”.
5. Nominatorsareresponsibletodistributetheresultsbacktotheproducer.6. NominatorswillreceivetheinitialfeeinvoicefromCDCB,basedonthefeecodeassigned.AI
servicefeeformalesbeingmarketedusingUSgenomicevaluationsshouldbepaidtoNAAB.
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1.5 Data Exchange through secure FTP CDCBandgenomicnominatorscanexchangedatathroughtheCDCBwebquerysystemorthroughasecureFTParea.Thewebqueryistypicallyusedwhenprocessingasmallnumberofrecordsorfewrecordsneedtobedisplayed.However,whenlargenumberofanimals/genotypesneedtobeprocessed,thistypicallyisdonethroughbatchsubmissions.FilesproducedbyCDCBareplacedinthe“out”directory.Filessubmittedbygenomicnominatorsareplacedinthe“in”folder”.
AfulldescriptionofthefilesgeneratedbyCDCBandplacedinthe“out”folderisavailableinhttps://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/CDCB_general_files_distributed_to_nominators.
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2.FeeCodeinformation2.1 How CDCB Collects Fees through Genomic Nominators TheCDCBgenomicfeesarestructuredtorewardproducersthatareprovidingthemostdataorinformationforthegreatestvaluetotheCDCBcooperatordatabase.Thecurrentfeescheduleencouragescontributorstonotonlymaintain,buttoincreasetheamountandkindsofdatatheyarecontributingtothesystem,toimproveaccurategeneticevaluations.
AllrequiredInitialFeesaretobecollectedbythegenomicnominator.TheAIServiceFeeiscollectedbyNAAB.AllfeescollectedwillbethenbeforwardedtotheCDCB.Thefemaleandinitialmalefeeswillbechargedonlytothefirstgenotypesubmittedfortheanimal.
Therewillbenorefundoffees,exceptforerrorsgeneratedbyCDCB.Evenifthegenomictestresultsdonotworktothesubmitter’ssatisfactionoramaleisnotplacedintoservice.
Thedetailedinformationisdescribedinhttps://www.uscdcb.com/wp-content/uploads/2016/03/CDCB-Fee-Schedule-Update-7-15-2016.pdf.TheCDCBhastwoonlineapplications(GT_Fee:https://queries.uscdcb.com/CF-queries/GT_Fee.cfm[PASSWORDPROTECTED]andgetfee:https://queries.uscdcb.com/CF-queries/getfee.cfm[PASSWORDPROTECTED])tohelpgenomicnominatorsdeterminingtheappropriatefeecodes(detailsin6.NominationandDataCorrectionUsingWebQuery).TheCDCBhasalsocreatedanapplicationtool“CDCBFeeSchedule”:https://www.uscdcb.com/fs_01/tohelpgenomicnominatorsdeterminingtheappropriatefeecodes.Finally,onthedaypriortothemonthlygenomicrelease,CDCBplacesfileNOMNAME_Check_Fee_Code_1705.csvinthe“out”directoryofeachgenomicnominatortoshowthefeeassignedtoeachindividualgenotyped.ThisfileisreviewedbyCDCBstaffandforwardedtotheCDCBtreasurerwhothenpreparestheinvoice,whichisthensenttothegenomicnominator.
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3.Nomination3.1 Nomination information NominationisoneofthemostimportantdataCDCBreceivesfromitsclients.NominationisaprocesswhereaseriesofcriticalinformationisincludedintheCDCBcollaboratordatabase:
• Pedigreeoftheanimal(ifthepedigreeisnotinourdatabasealready):Thepedigreeofananimalisimportantnotonlyfortheevaluationitselfbutalsotocheckforparent-progenyconflictsduringgenotypesubmission.Withoutknowingtheparentage,wearenotableconfirmthatthegenotypeisfromtheintendedanimal.Thisistheoneofthereasonswhynominationshouldbecompletedbeforesubmissionofgenotypes.
• AssociationbetweenthesampleIDandtheAnimalID:AssociationbetweensampleIDandtheanimalIDisextremelyimportant.Missingassociationwillnotallowlinkingthegenotypetothecorrectanimal(eventalsoknownas“genotypewithzerokey”).
• Providingthecorrectfeecode:Thecorrectfeecodeisrequired,inordertofairlychargefortheevaluation.Failingtoindicatethefeecodewillleavethefeecode“N”,whichmeans“noCDCBpredictionwillbedelivered,andnofeeimposed”.
• Providingcorrectparentageindicator:Theparentageonlyindicatorisnecessarytodeterminethetypeofservicerequired.Ifparentageonlycodeisdetermined,therewillbenofeesbilledtothenominator(andnootherservicereleased).
•
3.2. Nomination Through WebQuery TheCDCBwebquerycalledCDCB-Nomination_Qcanbeusedwhentheanimal’spedigreeisalreadyintheCDCBcollaboratordatabase(e.g.theanimalisinaDHIherd,orisaregisteredanimal1).
1) GototheAnimalQueries:https://queries.uscdcb.com/login2) Loginusingyourcredentials.Acceptthe“TermsofUse”3) ChoosetheCDCB-Nomination_Q(https://queries.uscdcb.com/CF-queries/Nom2.cfm)4) InputNominatorID(ifneeded),ParentageIndicator(PI),Group/HerdID,FeeType,AnimalID,
andSampleIDineachdesignatedboxlikeaboveandclicksubmit.(ParentageIndicatorandFeeType(code)areexplainedinhttps://redmine.uscdcb.com/projects/cdcb-customer-service/wiki#COMMONLY-USED-CODES)
1ItisunlikelyapedigreeisintheCDCBcollaboratordatabaseiftheanimalisregisteredwithaforeignbreedassociationotherthanCanada
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5) Iftheanimal’spedigreealreadyexistsintheCDCBcollaboratordatabase,parentageandthe
animal’snominationstatusaredisplayedasbelow.Ifthegenomicnominatorconfirmsthenominationinformationisallcorrect,thenbyjustclicking“AddThisNEWRecord”button,thenominationiscompleted.
6) Iftheanimal’spedigreeisnotintheCDCBcollaboratordatabase,thefollowingmessagewillbedisplayed.Byclickingon“Requestpedigreefromnon-CDCBsource”,promptsarequesttofindtheanimal’spedigreefromexternalsources,suchasbreedassociationsorInterbull.Thereturnedoutcome(ifany)canbeaccepted–andthenominationprocesscompleted-bycompilingtheinformationandclickingon“SubmitFormat1g”.
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7) Iftheexternalresearchoftheanimal’spedigreefailed,thegenomicnominatorwillhaveto
submitaFormat1throughtotheCDCBsftparea.8) Mostoftheinformationdisplayedcanbeupdated/corrected.Pleasebeawarethatnochanges
tofeecodeareallowedonceanevaluationhasbeenreleased.Forexample,the“SOLDfunction”allowschangingtherequesterIDafternominationiscompleted.However,pleasenotethatonlythecurrentnominatorcanperformthatchange.AnEmailwillbesenttothenewnominator,tonotifythechange.
3.3. Nomination Through secure FTP (SFTP) Whenalargenumberofanimalsneedtobenominated,submissionthroughSFTPisrecommended.
TheprocessisautomatedintheCDCBsystem.ThegenomicnominatorshouldsimplyplaceaFormat1/Format1Gfileinthe“in”directoryofhisSFTParea.Inordertoberecognized,thefileshouldbenamedaccordingtothefollowingconventions:
• ForFormat1,filesshouldbenamedasYYYYMMDD.1X,whereYYYYMMMDDistheyear,monthandday(e.g.20170101)andXcanbeeitheraletterornumber.
• Forformat1G,filesshouldbenamedasYYYYMMDD.1GX.
Oncethesubmissionisprocessed,a“notify”file(notify.YYYYMMDD.1(G)X)isplacedinthe“out”directory.Thisfilecontainsinformationoferrorsandthestatusofthesubmission.Incaseofa1Gfile,itcontainsinformationonthesuccess(ornot)ofthenominationprocess.
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3.3. Format 1 and Format 1G FullinformationonFormat1formatisavailableat:https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/Format_1
Format1istheCDCBstandardforapedigreerecord.Format1consistsoftheanimalidentification,sireidentification,damidentificationandcrossreferenceidentification,inadditiontosomeotherinformation,suchasbirthdate,sourcecode,andmultiplebirthcode.
Ex)Format1forBSUSA000068174286
0FBSUSA000068174286BSUSA000000198772BSUSA00006811717320160219B20160312P013HR000000BELLADEWSUGARPIEET
Format1GisaFormat1thatincludesnominationdata.AFormat1becomesaFormat1Gbyplacinga“G”atbyteposition88andbyincludingnominationinformation:
• sampleID@54-70• GroupID@130-137• ParentageIndicator@138• feecode@139• Herdcodedifferencereasoncode@140(ifapplicable).
Ex)0FBSUSA000068174286BSUSA000000198772BSUSA000068117173A1B2C3D4E5F620160219B20160312G013HR000000BELLADEWSUGARPIEET35051162N2
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CDCBstaffhasreceivedmultiplerequestsforclarificationsonthefollowingfieldsforFormat1andFormat1G:
RecordSourceCode(@79)-https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/Source_code:Sourcecodeisusedtoprioritizethedatasubmitted.SinceCDCBcanreceivemultiplerecordsforoneanimalfromdifferentorganizations,thesystemprioritizesthedatadependingonthesubmitter.Anorganizationwhithlowerprioritycannotcorrectrecordsmanagedbyahigherprioritysourcecode(“B”hasthehighestpriorityamongallorganizations).
RecordTypeCode(@88)-https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/Record_type_code:RecordtypecodeisusedtoindicatehowtherecordshouldbeprocessedbytheCDCBsystem.SinceFormat1cancontaindifferenttypesofinformation,indicationofrecordtypeisnecessary.SobyassigningRecordTypecode,genomicnominatorscanadd/delete/changetheinformationcurrentlystoredintheCDCBcollaboratordatabase.MultipleBirthCode(@91)-https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/Multiple_birth_code:MultipleBirthCode(MBC)shouldindicatethetypeofbirthoftheanimal.Thisinformationisusedtoverifytherelationshipwithitssire,damandsiblings.
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4.CommonReasonsfornotreceivinganEvaluation(andHowtoCorrecterrors)
Thereareanumberofpossiblereasonsthatpreventgenomicnominatorsfromreceivingageneticevaluationontheanimals.Thetwomostcommoncasesare:A)thegenotypeoftheanimalsisnotflaggedas“usable”,meaningthereareconflictspreventingtheCDCBsystemtousethegenotype,and;B)thenominationisnotcomplete(feecodeissetto“N”),meaningthenominationwasnotcompletedsuccessfully.Inthissection,thegenomicnominatorswillfoundasetofusefulinformationtopreventthatfromhappening.
4.1 Where to Find Genomic Confl icts Duringthegenotypeloadingprocess,theCDCBsystemchecksthequalityofthedata,suchasparent-progenyconflicts,Hardy–Weinberg equilibrium, missing information, and (many) more. It also generates report files to inform genomic nominators on what should be corrected for the genotype to be flagged as “usable”.Asdiscussedbefore,itisoneofgenomicnominator’sresponsibilitiestomakethegenotypeusable.
OnceaCDCBgenotypinglaboratoryloadsabatchofgenotypedata,genomicnominatorsreceivea.zipfilenamedLAB_YYYYMMDDXX.NOM.zip(ex.GSek_20170426A1.ABS.zip).Thefileisplacedinthegenomicnominator“out”directory.The.zipfilecontainssomeorallofthefollowingfiles:
• NOM_Nominator_Report.csv:Reportsonnumberoferrors/conflicts• NOM_Genomic_conflicts.htm:Animalswitherrorcodes(webversion)• NOM_Genotype_Conflicts.csv:Animalswitherrorcode(csvversion)• NOM_Parentage.csv:Parentageinformation• BB_LABCHIPYYYYMMDDX_No_Nomination.csv:animalswithmissinginformation• NOM_PGS_unlikely.csv:UnlikelyPGS(ifany)
Thefilecalled“NOM_Genotype_Conflicts.csv”containsamaximumof6errorcodesforeachsample.Animalsrarelyhavemorethan6conflicts,butitiscommonthatmultipleerrorsexistsforonesampleincludingerrorsrelatedtoitsparents,siblings,andgrandparents.
Columnsnamed“code[1-6]”indicatetheerrorcodesdescribingtheconflict(s)detectedforthegenotype(documentedin:https://redmine.uscdcb.com/projects/cdcb-customer-
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service/wiki/Genomic_error_codes).Columnsnamed“ID[1–6]”aretheID(s)relatedtothoseerrorsandconflicts.
TheNOM_Genomic_conflicts.htm(webbrowserfriendly)containsthesameinformationbutonamorehuman-friendlyview.
4.2 Common reasons for not receiving an evaluation
Genotype was not usable due to a confl ict, low cal l rate, being a crossbred (PI=“B”) Genomic conflicts are definitely themain reasons that prevent an animal from obtaining anevaluation(evenwhenthenominationwasdonecorrectly).Resolvingtheseconflictsisoneofthemostimportantrolesofgenomicnominators.Therefore,itisveryimportantfornominatorstounderstandthemeaningofconflicts/errorsreportedandhowtofixtheminordertomakethegenotypeusableforCDCBevaluations.Fulldocumentationontheseerrorscanbefoundathttps://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/Genomic_error_codesAs for the SNP-based test to detect crossbreds, documentation of the current thresholds isreferencedin:https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/CDCB_Genomic_Dictionary#Breed-conflict-determination
The genotype became usable after the genotypes were extracted for the evaluation CDCBreleases3typesofevaluations:weekly,monthly,andtriannualevaluations.Itisimportantthatgenomicnominatorsmakethenecessarycorrectionstotheirdatabeforethecutoffdeadline.ThelinkbelowprovidesdeadlinesandreleasedatesforCDCBevaluations.(https://queries.uscdcb.com/reference/sched.cfm)
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WeeklyevaluationsAweeklyevaluationisnotanofficialevaluation.Thepurposeofaweeklyevaluationistohelpproducersinmakingquickmating,culling,andmarketingdecisions.Thedatamustbeloadedby6:00pmonSunday.CDCBGenotypingLaboratorieshavetosubmittheirdataearlierthanthat,assubstantialprocessingtimeisrequiredtocontrollargefiles.Inthisevaluations,onlyanimalshavingausablegenotypeforthefirsttimebeforethedeadlinewillbeincluded.Nofurtherweeklyevaluationisprovidedafterthefirstonewasreleased.TheresultsarereleasedeveryTuesdayat~8:00am.MonthlyevaluationThemonthlyevaluationisofficial.Allqualifyinggenotypedanimalsareincluded.Noupdatesinthephenotypicrecordsareapplied.ThecutoffforthemonthlyevaluationisonSundayat6:00pmafterthegenotypesubmission+correctionweekandthereleasedayisthefirstTuesdayofthemonth(mightbedifferentduringthemonthsoftriannualevaluationsarereleased)at8:30am.TriannualEvaluationThetriannualevaluationsareofficialandarereleased…3timesayear:April,August,andDecember.Unlikethefirsttwoevaluationtypes,thisevaluationincludesnewphenotypicdata.Allanimals,genotypedorungenotyped,aredistributed.Theupdatedtraditionalevaluationsareaninputtothegenomicevaluationsystem.
The breed of evaluation is not among those we generate evaluations for Wecurrentlycalculate(G)PTAsfor5breeds:Ayrshire,BrownSwiss,Guernsey,Jersey,andHolstein.Toensureasmuchaspossibletoprovideaccurateevaluationresultstoproducers,CDCBperformsanapproximatebreedcheckforallgenotypedanimalswhentheirgenomicdataisprocessed.Thesystemchecksthatthebreeddeclaredinthesampleisthebreedwiththefewestunlikelybreedspecificalleles.Animalsfailingthischeck,stillcanbeincludedintheevaluationsiftheirBBR(BreedBaseRepresentation)valuesarehigherthan90%forthedeclaredbreed.However,sincethisvalueisobtainedduringtheevaluationofotheranimals,theevaluationforanimalsfailingtheapproximateSNPtest,butpassingtheBBRthresholdwillbedistributedtheweekafter.
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The animal’s genotype confl icted its imputed dam Since2016,genomicnominatorshavebeennotifiedwhenananimal’sgenotypehasaconflictwithitsdam’simputedgenotype.Unlesstheconflictisfixed,thisanimalwiththeconflictwillbeexcludedfromourevaluations.The“affiliatespecificgenotypereports”allowallgenomicnominatorstoobtainalistoftheseanimalsatanygiventime.
The fee code is “N (No fee paid)” or “H (Historic)” Feecode“N”meansthatnopaymentofafeehasbeenindicatedfortheanimal.Itwillnotbeevaluateduntiladifferentfeecodeisassignedtotheanimal.IfafeecodeisindicatedasH,thentheanimalisdesignatedashistorical.Theseanimalswithfeecode“H”areusedinthereferencepopulationtoincreaseaccuracyofestimates,butthoseanimalsdonotreceiveanevaluation.Referenceonavailablefeecodes:https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/Genomic_fee_codes
The bul l has semen marketed and it ’s not a tr iannual evaluation release Forbullsbeingmarketed,theevaluationisupdatedonlyforthetriannualevaluation:onApril,August,andDecember.
The owner of the bul l is not located in the US and AI service fee has not been paid, so the evaluation is not public CDCBdoesnotpublishforeignbulls’evaluationsunlessAIservicefeehasbeenpaid,inordertorespectthepoliciesofindividualcountries.
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The genotype is designated parentage verif ication only (PI=“P”) ReferenceonParentageverificationcodes:https://redmine.uscdcb.com/projects/cdcb-customer-service/wiki/Parentage_indicator_codes
The bul l is foreign, over 15months of age and no AI service fee has been paid GenotypedU.S.maleswillreceiveagenomicevaluationmonthly.Foreigngenotypedmalesreceiveagenomicevaluationmonthlyupthrough15monthsofagewiththegenomicevaluationonlyprovidedtothegenomicnominator.ForeignmalesmusthavetheAIServiceFeepaidtogetagenomicevaluationreleasedpublicly(oreventothenominatorpast15monthsofage).
Wrong animal ID EvaluationresultsaredistributedusingaspecificID,whichistheoneconsidered“preferred”intheCDCBcollaboratordatabaseforthatanimal.TheanimalIDconsistsofa2characterbreedcodeplus3charactercountrycodeanda12digitregistrationID,thereforeatotalof17digits.Iftheanimaliscrossreferenced,youmayneedtosearchforanalternateIDastherearesomequeriesthatdonotaccessthecrossreferences.
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5.WebQueries
5.1 What is Web Query and what can we do with it WebQueriesaretoolsdevelopedbyUSDA(AGIL)forcertifiedgenotypinglaboratoriesandgenomicnominatorstobeabletosubmitdataorquerydataeasily.Becauseofthesimplicityoftheusage,mostgenomicnominatorspreferusingthewebquery.ThedirectlinktotheWebQueriesis:
https://queries.uscdcb.com/login
MostfrequentlyusedqueriesareCDCB-Nomination(toadd/remove/updatenominationsandUPDATEgenotypeinformation),GenotypeQuery(toshow(andfix)theusability/errorstatusofreceivedgenotypes)andgenotypeMove/SwapAPP(tocorrectbadgenotypetoanimalassignments).Fordetailedinformationandinstructionsofthosequerieswillbedescribedinthenext10topics.
5.2 CDCB-Nomination_Q Asdiscussedbefore,CDCB-Nomination_Qisusedtonominateanimalsortochangeanominationstatusofanominationthatwasdonepreviously.Thefieldsthatcanbechanged(updated)usingthisqueryare:1) ParentageOnlyIndicator(PI)-OnlyfromPtoN(notvice-versa)2) FeeCode-OnlychangesallowedarefeecodesfromNtoacorrectfeecode.Incaseof
errorincludingthefeecode,thenominatorshouldcontactCDCBcustomerservice([email protected]).
3) NominatorID-Nominationinformation,asdescribedpreviously.4) Group/HerdID-usedtovalidatethefeecode.Itismostimportantfordomesticdatato
distinguishamongfeecodes1,2and3.
5.3 Aff i l iate specif ic genotype reports Listsgenotypeswithfeecode=Nloadedinthepast6months
Asmentionedbefore,theanimalwillnotgetevaluationresultswhenthefeecodeis“N”.ThisreportwilldisplaywhichanimalshavegenotypesloadedintotheCDCBcollaboratordatabase,butthefeecodeisN.
Feecodesforgenotypesloadedsincethelastinvoice
Thisreportwillsummarizewhichfeecodewasgiventowhichanimal/sampleID.
Listsparentageonlygenotypessincethepreviousgenomicrun
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Thisreportshowsanimalsindicatedasparentageonly(PI=P),whichdonotgetanevaluationincludinghaplotypeanalysis.
ReportsmissinganimalIDforarequester
ThisreportshowstheSampleID,dateofgenotypeloadedandchiptypeforthosegenotypesloadedwithoutvalidnomination.Thosegenotypeswillnotgetevaluated.
Conflictsforgenotypesloadedinthepast45days
Thisreportshowstheconflicts(includinggenomicerrorcodes)foranimalsthatwereloadedinthepast45days.
Checkformissingpedigreeofanimalsnominatedinthepast75days
ThisreportincludesanimalIDsthathavebeennominatedwithunknownparentsorunknowngrandparentsandtheirgenotypeshavenotarrivedatCDCByet.
Listconflictinggenotypeswithinanimal(negativekey)
Anegativekeyisgiventoagenotypethatisfoundtoconflictwithothergenotypesforthesameanimal,whentheanimalhasmultiplegenotypes.Sinceanegativekeygenotypeisnotincludedintheevaluations,re-assigningthenegativekeygenotypetothecorrectanimalisrequired.Ifanotherkeyisassignedtothegenotype,thenewanimalwillgetevaluatedusingthegenotype.
Animalswithunlikelygrandsire
Animalswithunlikelygrandsire(s)areexcludedfromourevaluation,inordertoavoidinaccuratepedigreeinformationbeingusedinourevaluations.UnlikelyMGS/PGSareindicatedas“U”(unlikely)andlikelyMBS/PGSareindicatedas“L”(likely)inthisreport.
Animalswithgenotypesthatconflictwithimputeddamgenotypes
Genomicconflictsbetweenananimalanditsdammakethegenotypeunusable;thereforethisinformationisreportedhere.
Parentageverificationrecordsforgenotypesloadedinthepast45days
Thisreportshowsparentageconfirmationandparentagesuggestionsofgenotypesloadedinthepast45days.Foranaccurateevaluation,itisimportanttohavecompleteparentage.
NominatorGRAPH
CDCBreportsnominators’performanceeverymonthandconductsnominatorperformanceaudit,inordertoensurethequalityofdataandtounderstandhow
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CDCBandnominatorsshouldbeimproved.Thegraphshowspast10monthperformanceofthenominator.Thedetailsofthecriteriaareindicatedin1.1ReportCards.
5.4 Check FMT1 records ThisquerychecksiftheFormat1(pedigree)providedmatchestheinformationintheCDCBcollaboratordatabase.
1. Enterthepedigreeinformat1formatintothetextboxandclicksubmit
2. Aboxincludingpedigreeinformationisdisplayed
3. Thefirstrow(“In”)therecordjustenteredisdisplayed4. Thesecondrow(“CDCB”)showstherecordintheCDCBcollaboratordatabase.5. The“matched”atthebottomoftheexample,meansthattheinformationmatches.
5.5 Check Dam Thisquerychecks animal pedigree and error information, and dam pedigree/progeny/calving
dates.Thisqueryisespeciallyusefultofindoutthereasonofdamnotbeingaccepted(orblanked),asmostcommonreasonsofrejectionofdamare:
a. AsiblingwhosharethesamedamhasaMBCwhichconflictwiththeanimals’birthdate/MBC.
b. Dam’sfreshdatadoesnotmatchwiththeanimal’sbirthdate/MBC.
1. Entera17-digitanimalIDoftheanimalthatthegenomicnominatorwantstoknowthedam’sinformationforandclicksubmit.
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2. Asummaryofthepedigree,existingpedigreeerror(s)andcurrentdam’sinformation(dam’spedigree,calvingdate(s),andprogenyandtheirbirthdateandMBC)isdisplayed:
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5.6 Get 116 parentage SNP for a l ist of animal IDs Thisquerywasdesignedforgenotypinglaboratories.Pleasedisregard
5.7 New Genotype Query Thisqueryisusedtoshowusabilityofthegivengenotypeandalsousedtofixshownerrorsifany.Correctingpedigreeinformation,basedongenomicerror(s)1. SubmittheanimalID,thegenomicnominatorwillbedirectedtothisscreen.This
showssamleinformation,genotypeconfirmations,andgenomicconflicts.
2. Ifthegenomicnominatorwanttofixtheconflicts,clickonFIX_FMT1.3. Step2willdirectyoutothenextscreenshowingsomesuggestionsthatyoucan
accept,inordertoresolvetheconflicts:
4. Thegenomicnominatorshouldcheckbeforeacceptingthesuggestionsandifthe
genomicnominatorthinksthatthesuggestioniscorrectthenyouwillclickthebox“submitchanges.”
5. Oncethechangeisprocessed,thegenomicnominatorshouldexpecttoseethatthepedigreeisupdatedandtheconflictsaregone(afternextupdateprogramrunsat
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noonand5:00am).Butitisrecommendedthatgenomicnominatorschecktheupdatedrecordstoseeifthedatawasupdatedasintended.
WithdrawingunusablegenotypeWithdrawalshouldbereservedforunusualsituationssuchasthegenotypeactuallycamefromabeefbreed,thereforethegenotypecannotbeassignedtoanyanimalintheCDCBdatabase,thereisnopossibilityofdeterminingwhichanimalthegenotypecamefromandthereisnopossibilitythatthegenomicnominatorwouldliketousethegenotype.Insuchsituations,youcanuseNewGenotypeQuerytodosobyclickingonwithdrawinUseIndcolumn.Pleasenotethatthereare5possibleusabilityindicatorsthatthiscolumncanhave,whichareY(Usable),N(Notusable),L(Lowcallrate),M(Multiple/usable),U(Unreliable)andgenomicnominatorshavetheoptiontowithdrawgenotypesonlywhentheUseIndcolumnisN,L,orU.
5.8 GT Fee GTFeeisusedtosearchforafeecodebasedonagivenherdID.Thequerywillshowfeecodeandkindofparticipationontheprogram.Thisqueryisusefulduringnomination,todeterminetherightfeecodeforeachanimal.
5.9 parentage.cfm Thisqueryoutputsparentageinformationinacommadelimitedfile(csv)fortherequiredanimal(s).
5.10 Genotype Move/Swap APP GenotypeMove/SwapAPPisusedwhenagenotypehastobere-assignedtoanotheranimal.AnimalIDorsampleIDcanbeused.Notethatan“S+”infrontofIDmeansthattheIDthatisfollowingS+isasampleID,notananimalID.
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Howtomoveagenotypeassignedfromanimaltoanother1. Oncequeried,bothanimalsthatareinvolvedinthe“move”aredisplayed.2. Allfieldsmustbeprovided,includingthegroupname.3. Oncesatisfied,click“ReassingGenotypes”
5.11 getfee ThisapplicationshowsthefeecodethatisassignedtoananimalID.ThisissimilartoGTfee,butbasedonanimalID.
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6. GenomicNominatorChecklist
1. Communicatewithyourcustomertoarrangesamplecollection2. Communicatewiththelabtocoordinatethefeeschedule3. NominateanimalsbeforethegenotypesaresenttoCDCB4. CheckifpedigreeandnominationweresuccessfullyloadedtoCDCBdatabaseby
checkingformat1E/notifyfile5. Correcterrorsfrompedigreeandnominationsubmission6. Oncegenotypesareloadedbythelab,checkexistenceofgenomicconflicts7. Resolvethegenomicconflicts,inordertomakethegenotypeusable8. Youshouldexpectweeklyevaluationresults(ifthegenotypewasnew)and
monthlyevaluationsifeverythingiscorrect.Sochecktheevaluationschedule9. Distributetheevaluationresultstoyourcustomersonceyoureceiveevaluation
resultsfromus
