Autosomal InDels for Ancestry
NEW: download consensus results AIM-InDels-2015 here
In agreement with the proposal voted in the last general assembly, this year will take place the first phase of the GHEP-ISFG Collaborative Exercise on the “Analysis of autosomal ancestry-informative indels”. In this phase the participating laboratories will be supplied with a primer mix needed to implement the technique and to genotype all samples included in the Intercomparison Exercise 2014 (kinship module, basic level). Implementing the technique properly and the correct genotyping of samples from this first step will allow the lab to access the second phase of the exercise that will be proposed in the forthcoming general assembly.
The genotyping methodology is straightforward and similar to that employed with STRs involving a single multiplex PCR followed by capillary electrophoresis (Pereira et al., 2012).
Laboratory work comprises the following steps:
1. Multiplex PCR. The 46 indel markers are amplified in a single PCR reaction using the primer mix provided. The primer mix is optimized to obtain balanced reaction products following the protocol indicated. The original protocol uses the PCR master mix "QIAGEN Multiplex PCR Kit."
2. Electrophoretic separation of amplified fragments. To be performed in a capillary sequencer such as "ABI Genetic Analyzer" (310, 3100, 3130, 3500, 3730 or equivalent variants). The original protocol uses POP7 as the separation polymer (alternatively, POP6 or POP4 may be used, always taking into account the consequent changes of electrophoretic mobility).
A properly processed sample should result in an electropherogram similar to that shown in the figure.
To the participating laboratories, an aliquot of 100 uL of PCR primer mix will be sent allowing the processing of approximately 100 reactions (mixture already prepared containing dye-labeled primer pairs needed for the co-amplification of the 46 markers). Any other materials or reagents required for the study should be obtained by the participating laboratory.
For additional information or doubts regarding the reaction protocol and genetic profiling, please contact Rui Pereira (firstname.lastname@example.org). Template files of "panels" and "bins" to import into the analysis program (eg. GeneMapper), including support for mobility adjustment of each apparatus, can be requested to the same email address.
The results must be submitted until one month after the deadline established for the GHEP Intercomparison Exercise 2014 including the genetic profile of the samples (in Excel format according to the template ) and the electropherograms in pdf format.
It is recommended to save the .fsa files and/or electrophoregrams of all runs performed as they may be needed to clarify questions that may arise.
* Note: in the second phase each laboratory will be prompted to characterize populations of interest for the 46 AIM-indels. For the publication of the final results there will be a limit of one author per laboratory for a minimum of 100 individuals sampled per population. There may be a maximum of two authors accepted per participating laboratory when data corresponding to at least two different populations are submitted, each comprising at least 100 samples.
Requirements for participants
- The participants must be GHEP members and have the membership fees up to date.
- Payment of the participation fee of 100 euros on time (online with credit card or bank transfer, according to http://www.gep-isfg.org/en/proficiency-testing/payment-procedures.html)
Deadline for registration: December 31st, 2013
Deadline for payment: February 7th, 2014
Deadline for submission of results: one month after the deadline established for the GHEP Intercomparison Exercise 2014.
Leonor Gusmão: email@example.com
Rui Pereira: firstname.lastname@example.org