Burt, Dave - The Roslin Institute - University of Edinburgh

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SNP Discovery for ArrayIllumina ultra highthroughputsequencingSequence alignment toreference genomeSNP detection: 78MSNPs (segregating inone or more lines)SNP selection(stage1): 24MSNP selection(stage2): 10MSNP selection(stage3): 2MSNP selection(stage4): 650K243 chickens from 24 lines, samplesin pools of 10-15 individuals;Av. coverage 7-17X per lineUsed new GGA genome assembly(still unpublished)Criteria: Samtools Phred score ≥ 20,MAF ≥ 5, coverage ≥ 5, variantpresent in at least 5% of the readsCriteria: Phred quality score ≥ 60Criteria: No other SNPs within 10bpat least on one side, uniformly pacedout according to genetic distanceCriteria: Predicted reproducibility inarray, 50:50 broiler and layer SNPsCriteria: True reproducibility,Mendelian inheritance, HWE, LD34
% of SNPsNumber of SNPs/cMNumber of SNP/KbDistribution of SNPs201510501 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 ZChromosome78M 24M 10M 2M2001501005001 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 ZChromosome78M 24M 10M 2M4000030000200001000001 2 3 4 5 6 7 8 9 10 11 12 13 14 15 17 18 19 20 21 22 23 24 25 26 27 28 ZChromosome78M 24M 10M 2M35
Page 1 and 2: Next Generation SequencingCurrent S
Page 3 and 4: First Generation SequencingFrederic
Page 5 and 6: Genetic Maps• Genetic markers (e.
Page 7 and 8: QTL Mapping• QTL not mapped preci
Page 9 and 10: Genomic Tools• Expressed sequence
Page 11 and 12: Genomic Tools• Expressed sequence
Page 13 and 14: Sequencing TechnologiesNGS technolo
Page 15 and 16: Clonal Single Molecule ArraysAttach
Page 17 and 18: Base Calling from Raw DataT G C T A
Page 19 and 20: Applications19
Page 21 and 22: Avian GenomesFlightSmall genomeUniq
Page 23 and 24: Computational Pipeline forEnsembl/C
Page 25 and 26: Changes in gene family size along e
Page 27 and 28: Compare Rates of EvolutionSelection
Page 29 and 30: Rates Mammals > Birdsmovement of B
Page 31 and 32: Applications31
Page 33: Genome Wide Selection• Genotype 1
Page 37 and 38: Annotation of SNPs%5045403530252015
Page 39 and 40: Final Panel Selection• 600K panel
Page 41 and 42: Applications of SNP Panel• Genomi
Page 43 and 44: AcknowledgementsFundingBBSRC/Defra
Page 45 and 46: RNA-Seq45
Page 47 and 48: Gene Models: TEF47
Page 49 and 50: Experimental Design• 3 spleen sam
Page 51 and 52: Differential Gene ExpressionGene Sy
Page 53 and 54: Enrichment Analysis: MicroarrayMicr
Page 55 and 56: Advantages of RNA-Seq55
Page 57 and 58: AcknowledgementsFundingBiotechnolog
Page 59: Applications59
Page 62 and 63: MeDIP-Seq: NPAS462
Page 64 and 65: Sequencing TechnologiesNGS technolo
Page 66: Sequencing TechnologiesNGS technolo

Burt, Dave - The Roslin Institute - University of Edinburgh

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