SEQUENCING SERVICES. McGill University and Génome Québec Innovation Centre MARCH 16, Version 4.0

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1 MARCH 16, 2014 SEQUENCING SERVICES McGill University and Génome Québec Innovation Centre SNP Validation and SNP discovery services Next-Generation Sequencing technology User Guide Version 4.0 Copyright 2014 McGill University and Génome Québec Innovation Centre All rights reserved.

2 Table of Contents TABLE OF CONTENTS... 2 INTRODUCTION... 3 SERVICE REQUEST... 4 QUOTE REQUEST... 4 SERVICE REQUEST FORM (NEW REQUEST)... 4 SERVICE REQUEST FORM (EXISTING ORDER)... 4 BILLING POLICY... 5 METHOD OF PAYMENT... 5 SAMPLE SUBMISSION REQUIREMENTS... 6 SENDING SAMPLES... 8 TRANSMISSION OF RESULTS... 9 FOR MORE INFORMATION Client Management Office Sequencing Services

3 Introduction This document describes the procedure for submitting samples for SNP validation and SNP discovery using Next-Generation Sequencing technologies. In order to use these services, an account must first be opened in our Web application Nanuq. Samples must then be sent to the Innovation Centre in accordance with the submission requirements described in this guide. 3

4 Service Request Quote Request Contact the Client Management Office for more information regarding prices or quote requests: Phone: Fax: Note: A contract is required for all services that total or exceed $25, (prior to taxes). Service Request Form (new Request) The new Request Form functionalities are used for new projects only. Login to your Nanuq account. In the Request Section, click Add new Request and follow the instructions. Do not use the Back button of your Browser to go back to previous pages. Use the menu on the left-hand side of the screen. The Request Form is completed when the Submit button is used, otherwise, its status will remain as Draft. Incomplete new Requests will become accessible in future sessions using Request List (see below). The work in the laboratory will only start when all required documentation is provided. Service Request Form (existing order) Login to your Nanuq account. In the Request Section, click Request List. This is used when 1) new samples or replacement samples are submitted as part of an existing project or 2) to continue entering out new information in a Draft Request. To submit new samples, go to the Sample Submission Section. From there, you can: Download empty templates for submitting new samples. Review previous sample submissions. Add comments about your samples. Do not add new samples or replacement samples to an existing template file. Do not use the Back button of your Browser to go back to previous pages. Use the menu on the left-hand side of the screen. 4

5 Billing Policy Projects that last no longer than 3 months will be invoiced at the end of the project. However, those that last longer will be invoiced at regular intervals. In either case, the billing information must be provided on the sequencing services request form. Method of Payment Payments can be made by cheque (purchase order mandatory) or credit card. The cheque must be addressed and sent to: Génome Québec 630, boulevard René-Lévesque, suite 2660, Montréal (Québec) Canada H3B 1S6 Important: A purchase order number is required for services that total or exceed $2, (prior to taxes). For security purposes do not enter the credit card information in the sequencing services request form. A separate form will be sent at time of billing. 5

6 Sample Submission Requirements Important general considerations It is crucial that the guidelines mentioned in the User Guide be carefully followed so that unnecessary delays can be avoided. Any and all samples that do not conform to the guidelines expressed herein may be refused without compensation. When submitting nucleic acids for sequencing using next - generation sequencing technologies, it is recommended to: submit samples of the highest possible quality and purity. resuspend DNA samples in nuclease - free water or in 10 mm Tris - HCl ph (no EDTA should be added as its presence may inhibit some enzymatic reactions). avoid resuspending samples in buffers containing detergents (e.g. SDS) or other additives that may inhibit enzymatic activity during the library preparation and/or sequencing reaction. quantify samples using the PicoGreen method. Nanodrop or other purely spectrophotometricbased methods tend to overestimate sample concentration, resulting in an inadequate amount of starting material. ensure that the volume of each sample be within the range specified in the DNA Sample specifications section. precisely measure and report the volume of sample contained in each well using the accompanying Service Request Form. Sample identification of the container(s) carrying the sample(s) must correspond exactly to what is specified in the Request Form. All correspondence regarding completed or on-going services must refer to the corresponding quotation number (beginning with SCI... ), or to the corresponding Nanuq Project Name. DNA Sample specifications Samples with concentrations inferior to those specified below must be concentrated by the client prior to shipment. Should the sample volume be inferior to the minimum volume specified below, it will either be diluted to an appropriate volume without prior client consent or will be refused. The client will be informed of samples that fail the QC and can submit replacement samples. Additional fees will be applied for sample QC for each replacement sample. The client may decide to proceed with sub-optimal amounts or quality of sample, but will accept all risks. Depending of the target regions amplification method, genomic DNA samples preparation for a SNP discovery project may vary: 6

7 Sample volume and concentration required for the Fluidigm Access Array System: It is important to provide sufficient amounts of good quality genomic DNA in order to complete the project in its entirety. The concentration of genomic DNA samples should be at least 50 ng/µl in a volume of 6 µl. An aliquot of 1ul per sample will be used for internal quality control. Volume and concentration required per sample using Double PCR: It is important to provide a sufficient amount of good quality genomic DNA in order to complete the project in its entirety. The concentration of genomic DNA samples should be at least 10 ng/µl in a volume of 10 µl. An aliquot of 1ul per sample will be used for internal quality control. Accepted formats for DNA samples/libraries Samples/libraries must be submitted in 96-well plates. Less than 12 samples could be submitted in 1.5 ml Eppendorf tubes. Only two types of 96-well plates are accepted: Eppendorf twin.tec, Full Skirt, Cat# PREFERRED Corning Thermowell GOLD, Full Skirt, Cat# 3752 SECOND CHOICE We recommend the following sealing films: Life Technologies MicroAmp Clear Adhesive Film, Cat# We can provide such plates and seals to local users upon request. Please inform the Client Management Office for such a request upon submission of documentation for the requested service. All plates must be clearly labeled with the quote number, name of PI, date shipped and must correspond exactly to what is specified in the Request Form. 7

8 Sending Samples The shipment must include a printed and signed copy of the Request Form. DNA samples should be sent on dry ice, unless otherwise instructed. Samples can be sent by courier or brought to the Innovation Centre in person from Monday to Friday between 8h00 AM and 5h00 PM at the following address: Sébastien Brunet McGill University and Génome Québec Innovation Centre 740 Dr.-Penfield Avenue, room 7300 Montréal, QC, H3A 0G1 Tel: , ext Fax: Samples crossing the Canadian border should be shipped early in the week as even expedited shipments may be held up at customs. All required documentation for customs must be duly included with the package. IMPORTANT! Only send aliquots (in sufficient amounts), not stock samples. Any amount of remaining sample material will be retained for a period of approximately 6 months after the requested service has been completed and will then be destroyed and discarded (libraries will be kept for at least 1 year). Leftover samples can be returned to researchers upon special request. Such a request should be made to the Client Management Office at the beginning of the project. All fees for returning the samples are the client s responsibility and expense. 8

9 Transmission of Results The sequence reads (in FASTA format) and a basic analysis of the data will be delivered by ftp or by an external hard drive (if provided in advance). Upon request, the Bioinformatics team can provide help for a deeper analysis of the sequencing data. The sequencing results are directly accessible via our Web application Nanuq. A partial report can be requested at all times during the project in order to see its progress. 9

10 For More Information Client Management Office McGill University and Génome Québec Innovation Centre 740, Dr.-Penfield Avenue, Room 7104 Montréal (Québec) Canada H3A 0G1 Phone: Fax: Sequencing Services Pierre Lepage, Ph.D., Manager Phone: Ext.: Fax: