The 454 and Ion PGM at the Genomics Core Facility
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The 454 and Ion PGM at the Genomics Core Facility. Dr. Deborah Grove, Director for Genetic Analysis Genomics Core Facility Huck Institutes of the Life Sciences Penn State University. Services DNA Sequencing Illumina, 454 and Ion PGM Next Gen Sequencing Microarray

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The 454 and ion pgm at the genomics core facility

The 454 and Ion PGM at the Genomics Core Facility

Dr. Deborah Grove, Director for Genetic Analysis

Genomics Core Facility

Huck Institutes of the Life Sciences

Penn State University


The 454 and ion pgm at the genomics core facility

  • Services

  • DNA Sequencing

  • Illumina, 454 and Ion PGM Next Gen Sequencing

  • Microarray

  • Genotyping – VNTRs, SNPs, Open Array

  • qPCR by Real-Time

  • DNA Synthesis

  • DNA Extraction and Storage of DNA from Buccal Swabs








The 454 and ion pgm at the genomics core facility

Next-Generation Sequencers:

Massively Parallel Platforms

  • Roche 454FLX+ v2.8 – 500 million bases per run, 800 to 1000 bases

  • Ion PGM 318 chip – 2 to 4 billion bases per run, 400 base length

  • (Ion Proton)


The 454 and ion pgm at the genomics core facility

Roche 454 – Next Generation Sequencer

  • Pyrosequencing

  • FLX+ v2.8 has 800 to 1000 bp read

  • 160 million bases per

  • full slide

454 FLX +


The 454 and ion pgm at the genomics core facility

454 Titanium Sequencing Applications

  • Whole Genome – Shotgun 500 ngs dsDNA

  • Whole Genome -- Paired-End (3kb, 8kb, 20kb) 15 to 30 ugs dsDNA

  • Amplicon/Metagenomics 5 ngs

  • Transcriptome RNA


The 454 and ion pgm at the genomics core facility

DNA Fragmentation by nebulization

Fragment End Repair

AMPure Bead Clean up

Adaptor-Ligation

Small Fragment Removal

Library Quality Assessment and Quantification


The 454 and ion pgm at the genomics core facility

Primer Sets for Metagenomics

  • 16s Bacteria

  • ITS for Fungus

  • 18s set for Fungus and other Eukaryotes, targeting Protists

  • Archaea targeting both Crenarchaeota and Euryarchaeota


The 454 and ion pgm at the genomics core facility

Amplicon Preparation

27F_M6CGTATCGCCTCCCTCGCGCCATCAGATATCGCGAGAGAGTTTGATCMTGGCTCAG

907R_M6TATGCGCCTTGCCAGCCCGCTCAGCCCCGTCAATTCMTTTGAGTTT


The 454 and ion pgm at the genomics core facility

16S Variable Regions

27F_M6CGTATCGCCTCCCTCGCGCCATCAGATATCGCGAGAGAGTTTGATCMTGGCTCAG

907R_M6TATGCGCCTTGCCAGCCCGCTCAGCCCCGTCAATTCMTTTGAGTTT


Amplicons
Amplicons

27F

518R

907R


The 454 and ion pgm at the genomics core facility

  • One Bead

  • One DNA library

  • NTPs, Taq etc.



314 chip
314 CHIP

316 CHIP


The 454 and ion pgm at the genomics core facility

Approximate Cost from Genome Library thru Sequencing

314 Chip 160 million bases, 400,000 reads

318 Chip 3 billion bases, 6 to 8 million reads

$1500 to $2000


Coverage
Coverage

Full Plate = 1 million reads, 300 million bases

½ plate = 500,000 reads, 150 million bases

1 Quad = 200,000 reads, 60 million bases



The 454 and ion pgm at the genomics core facility

Full Plate = 1 million reads, 300 million bases

½ plate = 500,000 reads, 150 million bases

1 Quad = 200,000 reads, 60 million bases

http://www.youtube.com/embed/yVf2295JqUg


Coverage2
Coverage

Full Plate = 1 million reads, 300 million bases

½ plate = 500,000 reads, 150 million bases

1 Quad = 200,000 reads, 60 million bases


The 454 and ion pgm at the genomics core facility

Full Plate = 1 million reads, 300 million bases

½ plate = 500,000 reads, 150 million bases

1 Quad = 200,000 reads, 60 million bases


The 454 and ion pgm at the genomics core facility

Full Plate = 1 million reads, 300 million bases

½ plate = 500,000 reads, 150 million bases

1 Quad = 200,000 reads, 60 million bases


The 454 and ion pgm at the genomics core facility

  • Applications

  • Bacterial and Viral Genomes

  • Amplicons

  • Ampliseq Panels for SNP variants


The 454 and ion pgm at the genomics core facility

  • Ampliseq Cancer Panel

  • Only 10 ngs or less

  • FFPE tissues

  • Single Cells

  • Libraries take 3.5 hours

  • 2800 hot spots


The 454 and ion pgm at the genomics core facility

  • Use Ion AmpliSeq Designer


  • The 454 and ion pgm at the genomics core facility

  • 314 Chip 160 million bases, 400,000 reads

  • 318 Chip 3 billion bases, 6 to 8 million reads


  • The 454 and ion pgm at the genomics core facility

    Pac Bio

    • No amplification required

    • Single molecule

    • Several thousand base reads

    • (4 to 20 kb)

    • Least GC-biased sequencing

    • Run time 30 minutes


    The 454 and ion pgm at the genomics core facility

    Applications

    • Genomes: Finish Genomes and improve assembly with extra long reads (4000bp average and up to 20,000)

    • Genomic Complexity: Allow haplotype expansion, full length transcripts and splice variants, repeat expansions, minor variants

    • Epigenome: Detects base modifications using kinetics


    The 454 and ion pgm at the genomics core facility

    Thanks to:

    The Huck Institutes of the Life Sciences

    Lloyd and Dorothy Huck

    And the others in the lab…