Informatics

The processes involved in handling, processing, storage, and communication of informatics can be tailor-made to suit your needs too. Below is a breakdown of how informatics can be stored, processed and integrated into your systems or networks.

It all starts with samples that have been either stored in our biorepository or sent to us directly for analysis. Regardless of whether they have been stored with us for days or decades, we are able to retrieve and analyse samples immediately as our labs and biorepository are both on premises, reducing overall turnaround times.

What informatics do you provide?

Using our cutting-edge platforms from Illumina, PacBio, Fluidigm, ClearDX and more, we can customise arrays or sequencing investigations to fit your requirements, whether they involve “off the shelf kits” or bespoke panels. Furthermore, we are able to accommodate a wide range of samples for testing from several different sources including:

• Human
• Mouse
• Rat
• Other animal species
• Bacteria
• Viruses

Below is a breakdown of the services from which informatics are generated, including secondary and tertiary analyses reports that can be requested:

Next Generation Sequencing

Services provided

• Whole Genome Sequencing
• Whole Exome Sequencing
• Long Read sequencing
• Custom panel design and sequencing

Comprehensive genome wide exploratory identification of genetic variants by short read or long read whole genome sequencing (WGS).

• Short read sequencing performed using our 2 Novaseq 6000 sequencers and long reads by 2 Pacbio Sequel IIe sequencers on board at IBX
• Variety of sample types can be analysed from several sample sources (human, rat, mouse, etc)

Targeted exploration of pathogenic genetic variants using short read whole exome sequencing (WES).

• Identification of common or rare benign and pathogenic variants and SNPs in protein coding regions of entire genome.

High sensitivity detection of disease associated genetic variants by designing and sequencing targeted custom NGS based panels for precision diagnostics and personalized medicine.

• Our Nextseq and Miseq instruments can sequence smaller targeted genomic regions to identify disease associated variants at high sensitivity.
• Hereditary disease panels
• Breast and Ovarian cancer panel

Senteion-based data analysis for identification, classification and reporting of genetic variants using state of the art variant detection pipelines.

• Very parallelizable and rapid.
• Using state of the art contemporary variant calling pipelines to process hundreds of samples in parallel reducing turn-around-time from weeks to hours.

Pacbio SMRT Link based analysis of long read sequencing data for identification of genetic variants and quantification of transcriptomic elements.

• Pacbio’s proprietary state of the art software for analysing long read data generated from the Sequel II platform
• Available services are Whole Genome Sequencing, Whole Exome Sequencing, Viral and metagenomic sequencing, ISO Seq for transcriptome sequencing.

Clinical curation and reporting of genetic variants by panel of certified clinical geneticists with Fabric genomics clinical curation system.

• Using Fabric Genomics to perform manual curation of variants identified by NGS technologies, here assays are performed in a GxP compliant environment. Fabric’s team of experts can then identify and classify variants according to their potential impact.

Confirmatory clinical testing for variants identified by NGS using qPCR, Sanger or MLLP based methods.

• Confirmatory testing of variants identified by sequencing experiments can be performed using qPCR, Sanger or MLLA based technology.
• Clinical reporting of confirmatory testing is also available.

Profiling of whole transcriptome profile using short read or long read transcriptome sequencing

• Total transcriptome or mRNA sequencing
• Gene and transcript level expression quantification
• Gene fusion and rearrangement detection
• Identification of non-coding RNAs like microRNA and LNC (Long noncoding) RNA
• Biomarker identification

Detection of hypo and hyper methylated genomic regions to identify epigenetic markers.

• Bisulfite sequencing using Illumina short read sequencing technology.

End to end comprehensive consultation around client’s sequencing needs provided by in-house subject matter experts.

• End to end consultation on sample size, recommendation of technology/platform per clients requirements, analysis pipeline, reporting tools, data transmission methods etc are all covered.

Microarray

• Genotyping of clinical research variants associated with disease and pharmacogenetics using Illumina GDA or Thermofisher PMDA/PMRA arrays.
• Genotyping of common and rare variants across the most commonly studied using multi ethnic global arrays (GSA).
• High-resolution DNA copy number analysis to detect gains, losses, loss of heterozygosity (LOH)/absence of heterozygosity (AOH), copy-neutral loss of heterozygosity (cnLOH), regions identical-by-descent, and mosaicism using state of the art microarray platforms.
• High density interrogation of hyper and hypo methylated genomic regions using Methylation arrays.
• Gene and transcriptome level quantification using gene and exome arrays.
• Custom microarray design and analysis – based on client’s needs.

qPCR data analysis – Star allele determination and CDISC formatted outputs.

Sanger data analysis and reporting

How is my raw data processed?

The first step undertaken is to deliver the raw data to clients, this ensures transparency as well as giving you the ability to forecast or predict what level of processing is required for the data that has been collected.

The next step involves secondary analysis, for example, data generated from genotyping/gene expression by sequencing and methylation sequencing will require reads to be aligned to respective reference genomes. Similarly, VCF files will be generated from any genotyping by arrays.

Reports from tertiary analysis are listed as follows:

• Genotyping by array – PLINK Analysis and Imputations

• Genotyping by sequencing – gVCF files, Structural Variant reports, Copy number variants reports

• Gene expression by arrays – Differential Gene/Transcript expression profiling and statistical analysis

• Gene expression by sequencing – Gene/Transcript level quantification, Differential expression analysis

• Methylation by array – Methylation report

• Methylation by sequencing – Methylation report, differentially methylated sites analysis

The fourth and final form of analysis involves custom post processing which is requested on a case-by-case basis. Typically, these include:

• Genotyping – QC metrices are reported and custom panel analysis can be included upon request

• Gene Expression – Pathway analysis/Gene Enrichment analysis

• Methylation – Available upon request

How is my raw data/reports stored and shared?

There are two forms of informatics storage we offer at Sampled. Raw data/reports can be stored physically on our highly resilient Dell EMC Isilon storage system which can hold up to 1.2 Petabytes. Additionally, we offer cloud-based storage system – AWS S3, here data can be encrypted upon request. In either format, data can be stored and retrieved at any time by clients and removed from our databases upon request too.  

Generating and storing your informatics is important, but we also believe in the importance of seamless client integration, one example of this is how we integrate with clinical EHR systems (for hospitals, clinics etc.) to receive test orders into a HIPAA compliant and secure server using the HL7 protocol. Moreover, test results can also be sent back to HER systems via end-to-end encrypted HL7 messaging through private VNP tunnels. If you have specific platform or system integration requests, we are always willing to accommodate these requirements where possible.

Alongside HL7 based encrypted messaging, Sampled supports a variety of transmission protocols including SFTP based transmission (which includes SFTP setup for clients) as well as API based result transmission (including custom API set up for clients)

Electronic Health Record data transmission via HL7

Sampled supports bidirectional controlled PHI data transmission to and from Sampled using HL7 standards on a secure end to end encrypted network. We provide integration support to our clients for connecting and sharing test results using HL7 protocol.

Data warehousing and integration of multi-omics data

We provide data warehousing services and help integrate client data coming from multiple technologies to a single platform, this could include Genomic, transcriptomic, proteomic, lipidomics data etc. This data warehousing service enables users to interrogate their population in a variety of ways to identify patient cohorts, share data, and run additional analysis on banked specimens at Sampled.