DNA Library Preparation and Sequencing

Human Whole Genome Sequencing

• Illumina TruSeq DNA PCR-Free Library Prep Kit as standard workflow
• Illumina TruSeq DNA Nano Library Prep Kit for low input samples

Whole Exome Sequencing and Targeted DNA Sequencing

Libraries are prepared using: 

• Roche KAPA HyperPlus Kit with UMI-containing adapters

Enrichment is performed using:

• Twist Comprehensive Exome Probe Panel for Whole Exome Sequencing
• Any Twist Custom Probe Panel or predefined probe panel targeting genomic area of interest

Small Genome Sequencing

• Illumina DNA Prep, Tagmentation Kit (previously called Nextera DNA)

If you are interested in collaborating with us on development of new protocols, or if you have a suggestion for the implementation of a novel method, please contact tina [dot] catela_ivkovic [at] med [dot] lu [dot] se (Tina Catela Ivkovic).

General information before starting a DNA Sequencing project

• DNA should be of high quality and diluted in water or EB buffer, presence of EDTA in the storage buffer might affect the library preparation.
• DNA isolated from FFPE samples must be of high quality, QC needs to be performed by a qPCR-based method (available at CTG).
• DNA should be of high purity, recommended OD260/280 of 1.8-2.0 and OD260/230 of 1.8-2.2 based on spectrophotometric measurement (e.g. by Nanodrop).
• All samples must be diluted/normalized based on concentration measurements performed by a fluorometric method (e.g. Qubit). Measurements based on spectrophotometric method (e.g. Nanodrop) are not acceptable.
• When requesting a project in iLab please specify the required sequencing depth for each sample.

For Whole Exome and Targeted DNA Sequencing

• Up to eight samples/libraries are pooled prior to the enrichment step.
• The price for this particular part of the project is calculated per pool. (For example, if you have 9 samples this would be calculated as two pools).
• If you are interested in custom probe pools for targeted sequencing, contact us for more information.

Sample input

• DNA input amounts differ between assays. Please see the table below for required sample concentration and delivery volumes. Lower concentrations and volumes can be discussed.
• Always dilute samples in nuclease-free H₂O or EB buffer.

Delivery of samples to CTG

DNA should be delivered aliquoted on ice in:

• an 8-tube strip labeled with Sample ID or Sample number (i.e. 1, 2, 3...) on the lid and side of the tube. 
• a fully skirted 0.2 ml plate with cold resistant seal (can be provided by CTG). Samples bust be placed column-wise (A1, B1, C1...)

Requesting a project at CTG

To initiate a project using our available services, please start a project in iLab. You can login using your LucatID (SWAMID) on the Lund University iLab webpage.

Data management and additional analysis

CTG uses secure LSENS servers hosted by LUNARC, center for scientific and technical computing at Lund University facility, for internal data management and analysis.

Delivery medium

• All data is by default delivered to the customer via a dedicated secure file server hosted on Lund University.
• For an additional cost, data can be delivered on a hard disk.
• For alternative options, please send us an inquiry.

Data storage

After data delivery, data will be kept by CTG for 3 months and subsequently deleted. We strongly recommend you to backup your data, i.e. have at least two copies. CTG cannot help you if your data gets corrupt or lost!

Additional Services

For additional Bioinformatics services please contact NBIS – National Bioinformatics Infrastructure Sweden, (https://nbis.se/).