myGenomics (CLIA Compliant)

Turn-around 10-20days. No minimum sample requirement.

Initial sample QC, Illumina indexed library preparation and paired-end sequencing using the NextSeq v2 platform. Delivery of FASTQ data files via cloud.

Data analysis if needed is available and will deliver VCF (variant call file) with BWA mapping and GATK variant call information. Included filters are variant allele frequency (1000 genome), known pathogenic variants (dbSNP) and suspect variants (frameshift, stop gain, stop loss), SIFT score, Polyphen score. Additional deliverables include: initial sample QC, fragmentation QC, library prep QC, sequencing reads QC, coverage and FastQC plots.

Turn-around 10-20 business days. No minimum sample requirement.
Price includes: initial sample QC and indexed Illumina library preparation with capture using Agilent SureSelect AllExon v7. ~50X coverage (5G) generated using paired-end reads sufficient to cover 80% exons >20x. Delivery of FASTQ data. Data analysis available.

The Agilent SureSelect Focused Exome design is highly targeted panel that enables deep coverage of only those regions within the human genome that have been associated with disease, allowing you to focus on mutations that matter.

5,000 Disease Associated Genes; 100x coverage; 95% targets covered > 20x

Service includes:
Initial sample QC on Nanodrop, Qubit and visualization through agarose gel electrophoresis.
Illumina Iibrary preparation, library QC
Agilent SureSelect Focused Exome capture, capture QC
Paired-end sequencing on Illumina NextSeq, FastQC
1.5G ± 0.15 data per sample

Project Details:
Customer submitted gDNA: >2ug; min. 25ng/ul;
Data will be delivered via Google Drive/Base Space as unanalyzed FASTQ files unless data analysis requested for additional $50/sample.

Turnaround time:
For acceptable samples, turn around time for delivery of FASTQ files is 10-20 days from initial QC of sample.

No minimum sample volume requirement.

OneSeq - One assay for genome-wide CNV, LOH, Mutations, SNPs, InDels:

Agilent's OneSeq target enrichment panel is revolutionizing cytogenetic research by providing one assay for wide spectrum of genetic variations in Constitutional Diseases (e.g. monogenic disorders, developmental disorders, intellectual disabilities) allowing to:
Detect copy number changes at a targeted resolution of 300kb in a genome-wide backbone
Detect copy number changes at a targeted higher resolution of 25kb– 50kb in disease-associated ClinGen regions
Detect genome-wide LOH as small as 5Mb
Detect mutations, SNPs and InDels

Sample to data in 20-30days. Data analysis if needed is available at $200/sample.

NGS technologies are able to provide high genome coverages at a relatively low cost. However, due to limited read length, de novo assembly often leaves gaps or fails to distinguish circular genomes from linear. myGenomics can fill this gap by combining standard library prep (PE100) with a single (3-5Kb) mate-pair library followed by sequencing at high depth coverage for Whole Genome Sequencing. The mean sequencing depth coverage for this service is >100x for smaller genomes (up to 5Mb). Sequencing is performed on an Illumina platform and data analysis delivering assembled genome (FASTa file) is included. 2-5 micrograms of single species specific purified DNA required.

Turn-around 10-20days from sample received to FASTq data delivered. No minimum sample requirement.

Data analysis $100/sample will include:
Gene expression report, FPKM values (TopHat),
Differential gene expression report comparing samples (CuffDiff),
Single Nucleotide Variation discovery
Fusion Gene Detection
Turn around time for analysis: 1 week
Pathway identification (additional price)

Additional deliverables
Initial sample QC, cDNA Library prep QC, Fragmentation QC, Sequencing reads QC, Coverage and FastQC plots.

RNA-seq can provide a profile of RNA presence, quantity, and sequence at a given moment in time or under specific conditions. Applications include:

• Gene Expression, identification of alternative gene spliced transcripts
• Differential Gene Expression comparing control and test conditions for example
• Pathway analysis to identify metabolic pathways affected under test conditions
• Single Nucleotide Variation Discovery
• Post Transcriptional Variations
• Fusion Gene Detection
• Transcriptome assembly of novel genomes

We offer a variety of services to best meet your budget and experimental needs.
Universal RNA-seq: Strand specific sequencing which includes polyA, long non-coding RNA, non-adenylated RNA, smRNA.

PolyA RNA-seq: Selective enrichment of poly-adenylated transcripts for cDNA preparation. Strand bias is not conserved.

Whole Transcriptome: Selective depletion of rRNA is followed by cDNA preparation allowing detection of lncRNA as well as mRNA. Strand bias is not conserved.​

Strand-specific library preparation: ​Ligation of unique adapters to the 5'- and 3'-ends of RNA fragments allows discrimination of the template DNA strand. This can be applied to either polyA or whole transcriptome projects.​​​

smRNA-seq/miRNA-Seq: Similar to strand-specific library preparation, with size selection to limit insert size of 19-21nt.

Normalized libraries: Treated with duplex-specific nuclease (DSN), resulting in under-representation of highly expressed transcripts, allowing detection of less abundant transcripts. Not suitable for experiments that need to retain expression profiling information.

Custom Target RNA-Seq: ​Please inquire with a list of target of interest.

myProfile:
Whole Genome
Whole Exome
Focused Exome (5,600 disease associated genes)
Whole Transcriptome (RNA-Seq)
​myBiome: Metagenomics
ChIP-Seq​

Cancer Genomics:
Breast, Ovarian, Prostate, Lung, Liver, Colorectal
Cancer HotSpots & Comprehensive testing

Gene Panels:
myMedAct Panel (57 Clinically actionable genes)
myRxAct Panel (Drug metabolism genes)
Hereditary Inclusion Body Myopathy Panel
Custom Targets

SNP Genotyping:
Apolipoprotein E, Factor V Leiden, ​Prothrombin ​

Turn-around 10-12days from sample received to data delivered. No minimum sample requirement. Price includes initial sample QC and indexed Illumina library preparation with capture and sequencing of BRCA1 and BRCA2 genes. ~100X coverage generated using paired-end reads. Delivery of FASTQ data. Analysis available for $50/sample. DNA extraction available for $20/sample. Bulk order discounts available.

Initial sample QC and cancer hotspot exome sequencing using Illumina'sTrueSeq Cancer Kit. 0.15G of data generated using NextSeq paired-end reads (>100X).  Delivery of FASTQ data.  Analysis available, please inquire. 

Quantification of DNA and RNA using Agilent screen tape and Tapestation.
Genomic DNA: $10/sample
High Sensitive DNA: $10/sample
High Sensitive RNA: $10/sample
Min. 10 samples. QC report delivered through email.

High sensitive DNA quantification using fluorescence based Qubit assay following manufacturer's instructions (Invitrogen). Min. 10 samples.

DNA extraction and QC from cells, body fluid, blood, saliva or tissue. Extraction from FFPE samples will be $30/sample. Volume discounts available.

Initial sample QC using Agarose gel electrophoresis, Nanodrop and Qubit assays.
DNA fragmentation on Bioruptor and QC on Tapestation.
Indexed Illumina library preparation and QC on Tapestation. Agilent Bravo liquid handler employed for high throughput library preparation. All QC reports delivered.

Capture and analysis of coding regions of 57 medically advisable genes including UTRs, with QC reporting. ~100X coverage generated using MiSeq paired-end 100nt reads. Delivery of FASTQ data. Analysis available, please inquire. Turn-around <2 weeks.

MLPA BRCA analysis

Multiplex Ligation-dependent Probe Amplification detecting abnormal copy numbers of BRCA1 and BRCA2

Extraction of total RNA including small RNA from cells, blood or tissue and QC on tapestation including electropherogram, concentrations and RIN values.

Sanger sequencing of your target area. Customer to provide DNA and primers for target area. Sequence generated on ABI 3730XL. Insilico amplicon design and primer synthesis available.

Initial sample QC and indexed Illumina library preparation. ChIP or genomic DNA accepted as input. No capture. Turn around <1 week.

High quality plasmid mini, midi and maxi preps. 10days turnaround time.