HudsonAlpha Discovery offers DNA profiling services through next-generation sequencing and microarray analysis.
Next-generation sequencing services include whole genome sequencing, exome and custom capture, whole genomic methylation analysis,
and profiling of amplicon, ChIP, or 5C/4C/HiC DNA fragments. Microarray services include SNP arrays
and methylation analysis.
Upon arrival to HudsonAlpha Discovery, all DNA samples are evaluated for concentration by Qubit® or Picogreen® and
for integrity by 2100 Bioanalyzer, Caliper GX, or agarose gel. Before submitting samples, please
review HudsonAlpha Discovery sample submission requirements.
Next-generation sequencing
Choosing the correct DNA sequencing service for your samples is dependent on the organism, total DNA available
for input, and project goals. For questions regarding experimental design or DNA service options please
contact us. If you plan to build a genome,
please discuss your project with us before submission as there are special considerations for such a project.
We currently offer:
Whole genome sequencing of any organism. The NovaSeq 6000
sequencers are available for whole genomic sequence of any organism
at any coverage. A customer can purchase partial lanes, full lanes,
or full flow cells of the S4 flow cell at PE100 or PE150. The NovaSeq
6000 platform is open to all organisms and all coverage options.
Whole genome sequencing for assembly of a novel genome. The
method of assembly dictates the types and construction of libraries for
sequencing. HudsonAlpha Discovery offers standard WGS libraries with different
insert/fragment sizes, and mate pair libraries.
Please verify the library construction requirements for the assembler of
choice before submitting samples, since many assemblers have very
specific requirements for the construction of the libraries providing
sequence. For example, assembler
ALLPATHS
requires data from two distinct library types made
from the same sample, both a mate pair library with a specific insert size as well as a standard library
with a specific insert size. HudsonAlpha Discovery uses Illumina's
Nextera Mate Pair kit for construction of mate pair libraries. It
offers a gel-free (non-size selected) protocol to use when input DNA is
limiting and a size-selected protocol to generate mate pair libraries of
size ranges 3-5kb, 5-7kb, or 7-10kb. Mate pair libraries may be
sequenced on all Illumina sequencers. The fastq files require special
processing before use in alignment or assembly analysis.
This technical note from Illumina describes the mate pair library
construction and data processing required. Adapter sequences used in
mate pair library preparation may be found
here.
Exome sequencing, which aims to reduce the complexity of sequencing the human genome down to the coding
regions. Our standard capture is the NimbleGen SeqCap EZ Exome Library v3.0. Other exome captures may be performed, but customers must purchase entire kits of the baits as we do not stock them. We currently offer the following exome capture services:
Product Name
Capture Size
Agilent SureSelect All Exon v5+UTR
75Mb
NimbleGen SeqCap EZ Exome Library v3.0 (standard)
64Mb
Custom capture, which is designed to isolate and deep-sequence a specific region of the genome
For in-solution capture, HudsonAlpha Discovery offers
Agilent SureSelect Target Enrichment
and NimbleGen SeqCap EZ Library
captures. Since all reactions occur in a plate, this method is much more
amenable to large projects than an array-based method. These products can be used in conjunction
with Illumina sequencing.
Whole genomic bisulfate sequencing (WGBS) can allow detection of 5mc, 5hmc, and/or 5fc methylation across a genome. Please see Methylation Services for more information.
Sequencing of ChIP/amplicon/4C/5C/HiC/other DNA HudsonAlpha Discovery does not perform ChIP or 4C/5C/HiC protocols,
but will create a sequencing library from the DNA obtained from those protocols and sequence it to the
requested specifications.
HudsonAlpha Discovery offers several array-based solutions for profiling DNA.
Genome-wide SNP mapping is best for large studies of hundreds of samples or more, since finding
high-confidence results usually requires high numbers of cases and controls. HudsonAlpha Discovery offers
Illumina Omni arrays
Minimum sample sizes may apply, depending on the array used.
Affymetrix Axiom Genotyping Solution offers the highest throughput. It utilizes the GeneTitan
instrument to process up to 750 samples per week.
Panel assays to query a known panel of SNPs, MNPs, or indels following a whole-genome SNP mapping experiment.
HudsonAlpha Discovery offers this service through the Infinium iSelect platform.
SNP validation HudsonAlpha Discovery offers real-time PCR services for validation of gene expression or genotyping results
using either TaqMan technology or SYBR Green I technology.
Methylation analysis HudsonAlpha Discovery offers the
MethylationEPIC BeadChip
to interrogate over 850K methylation sites at single-CpG-site resolution. This BeadChip is multiplexed, providing 8 arrays per slide. A minimum batch size of 32 is required to process the BeadChips. Fewer samples
may be submitted, but there may be delays in processing to create a batch to complete a slide. Please see Methylation Services for more information.
QC and data normalization is included in the cost of the assay. The intensity data is provided
for the A and B probes at each CpG which are used to calculate the "beta" value, or percent
methylation at each CpG. A p-value table is also provided, which is the detection p-value for each
CpG in each sample. There is also an annotation table that lists each CpG, and which genes it is
closest to, including the region of the gene (1500 bases upstream of TSS, gene body, 3'UTR, etc).
Some have more than one gene annotation depending on where it sits, and there is a column for
proximity to a CpG island. Additional interpretation or statistical analysis of results can be
requested for an extra fee.
