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Genomics & Transcriptomics

Overview

The Genomic and Transcriptomic (GT) Unit at CAAD is aimed at producing and analyzing data in the genomic and transcriptomic field obtained with NGS and/or arrays, both for UPO researchers as well as external users.

UNIT staff supports users in designing, performing and interpreting high-throughput genomic and transcriptomic experiments for biomarker discovery and/or analyses of multifactorial and  monogenic traits.

GT Unit operates tightly with Bioinformatics Unit at CAAD and offers an integrated pipeline which covers the entire process from the purification of nucleic acid from biosamples to the bioinformatic interpretation of the results. In addition, the Unit offers the interpretation of the genomic results and the preparation of the medical report, suitable for genetic counseling, to medical specialists, patients and researches. 

Equipment

The Unit is equipped with the following instruments:

·      Next Generation Sequencing Instruments:  Illumina MiSeq System and NextSeq 550 Sequencing System .

·      Infinium Option Starter kit for the manual preparation and scanning of the Infinium BeadChip arrays such as Infinium® HumanCytoSNP-12, CytoSNP-850K, HumanKaryomap-12 BeadChips, for the identification of Copy Number Variant in human diseases, and the Methyl EPIC 850 array for whole genome human methylation assay of 850,000 CpGs

·      SeqStudio Genetic Analyzer (ThermoFisher Scientific, Life Technologies) for Sanger sequencing and DNA fragment analysis for applications such as Microsatellite/tandem repeat sizing and genotyping, MLPA assay

·      Real time PCR Bio-Rad CFX384 qPCR and  Bio-Rad CFX96 qPCR Instrument, droplet digital PCR (ddPCR, QX200 Bio-Rad)

·      Agilent TapeStation (TapeStation 4200), a system for sample Quality Control during NGS workflows

·      Automatic workstation for liquid transfer (Tecan Freedom EVO100) 

Services

This Unit offers laboratory and computational support for all the main type of high-throughput NGS sequencing analysis such as target sequencing of gene panels, whole exome sequencing, mRNA and microRNA- sequencing. In addition, the Unit offers Sanger sequencing as well as support to nucleic acid purification and quantification.

The Unit offers diagnostic tests using either validated genetic diagnostic tests as well as new genetic tests developed and validated within projects of the Institute as well as upon requests from external laboratories and partners.

These analyses are mainly based on a local implementation of state-of-the-art NGS sequencing pipelines. In addition to that, the Unit offers consultancy for non-standard analysis and support over long-term projects. 

Type of Access

No access to the instrument infrastructures is allowed for external users, due to security reasons.

Prices

Description

kit

Unit

Minimum Number of Samples

Instrument

UPO users (euro)

Externals (euro)

Note

Clinical Exome

Trusight One expanded (6000 genes)

single sample

12

Nextseq550

490

613

costs cover library preparation and sequencing run

Clinical Exome

Trusight One  (4000 genes)

single sample

24

Nextseq550

290

363

costs cover library preparation and sequencing run

whole exome sequencing

Nextera Flex for enrichment and IDT probes

single sample

8

Nextseq550

622

778

costs cover library preparation and sequencing run

target sequencing (custom panel)

sureselect custom tier1 (1-499kb)

single sample

10

Miseq/ Nextseq500

440

550

costs cover library preparation and sequencing run.

A representative  custom panel is quoted. Gene panels with different sizes can  be designed and quoted on request

mRNA-seq ,  mRNA 50M reads/sample

TruSeq™ Stranded mRNA Library Prep  + TruSeq™ RNA Single Indexes Set A

single sample

8

Nextseq550

440

550

costs cover library preparation and sequencing run

micro RNA Seq 10M reads /sample

TruSeq™ Small RNA Library Prep Kit -Set A, Set A: indexes 1-12)

single sample

12

Nextseq550

165

206

costs cover library preparation and sequencing run

Sanger Sequencing

single sample

16

SeqStudio

6

8

costs cover sequencing (run and sequencing reaction and purification) of a PCR or a plasmid DNA/cDNA fragment

DNA fragment analysis

Microsatellite/tandel repeat sizing and genotyping, MLPA assay

single sample

16

SeqStudio

2

3

costs cover run  of a PCR  fragment

 

NGS Single Run Quotation

 

 

Description

kit

Instrument

UPO users (euro)

Externals (euro)

400M reads 2x150

NextSeq™ 500/550 High Output Kit v2.5 (300 Cycles)

Nextseq550

4566

5708

400M reads 2x75

NextSeq™ 500/550 High Output Kit v2.5 (150 Cycles)

Nextseq550

2884

3605

130M reads 2x150

NextSeq™ 500/550 Mid Output Kit v2.5 (300 Cycles)

Nextseq550

1803

2254

130M reads 2x75

NextSeq™ 500/550 Mid Output Kit v2.5 (150 Cycles)

Nextseq550

1153

1441

25M reads 2x300

MiSeq™ Reagent Kit v3 (600-cycle)

Miseq

1569

1961

15M reads 2x150

MiSeq™ Reagent Kit v2 (300-cycles)

Miseq

1090

1363

15M reads 2x250

MiSeq™ Reagent Kit v2 (300-cycles)

Miseq

1216

1520

1M reads 2x250

MiSeq™ Reagent Nano Kit v2 (500-cycles)

Miseq

404

505

1M reads 2x150

MiSeq™ Reagent Nano Kit v2 (300-cycles)

Miseq

347

434

4M reads 2x150

MiSeq™ Reagent Micro Kit v2 (300-cycles)

Miseq

492

615

 Service traceability

Analysis and result layouts are provided by appropriate software.

 Contacts

sandra.dalfonso@uniupo.it