RADseq paper

[Caitriona McInerney]

Dear All,

I thought you might find this paper interesting.

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. 
http://onlinelibrary.wiley.com/doi/10.1111/mec.12276/full

I have attached the main paper PDF and supplementary information.

Best regards

Caitríona McInerney

[Claudius Kerth]

Thank you Caitriona,

that's a great paper. I know of two other papers which also address this problem (at least for some of the statistics):

@ARTICLE{Gautier2012,

  author = {Mathieu Gautier and Karim Gharbi and Timothee Cezard and Julien Foucaud

and Carole Kerdelhué and Pierre Pudlo and Jean-Marie Cornuet and

Arnaud Estoup},

  title = {The effect of RAD allele dropout on the estimation of genetic variation

within and between populations.},

  journal = {Mol Ecol},

  year = {2012},

  month = {Oct},

  abstract = {Inexpensive short-read sequencing technologies applied to reduced

representation genomes is revolutionizing genetic research, especially

population genetics analysis, by allowing the genotyping of massive

numbers of single-nucleotide polymorphisms (SNP) for large numbers

of individuals and populations. Restriction site-associated DNA (RAD)

sequencing is a recent technique based on the characterization of

genomic regions flanking restriction sites. One of its potential

drawbacks is the presence of polymorphism within the restriction

site, which makes it impossible to observe the associated SNP allele

(i.e. allele dropout, ADO). To investigate the effect of ADO on genetic

variation estimated from RAD markers, we first mathematically derived

measures of the effect of ADO on allele frequencies as a function

of different parameters within a single population. We then used

RAD data sets simulated using a coalescence model to investigate

the magnitude of biases induced by ADO on the estimation of expected

heterozygosity and F(ST) under a simple demographic model of divergence

between two populations. We found that ADO tends to overestimate

genetic variation both within and between populations. Assuming a

mutation rate per nucleotide between 10(-9) and 10(-8) , this bias

remained low for most studied combinations of divergence time and

effective population size, except for large effective population

sizes. Averaging F(ST) values over multiple SNPs, for example, by

sliding window analysis, did not correct ADO biases. We briefly discuss

possible solutions to filter the most problematic cases of ADO using

read coverage to detect markers with a large excess of null alleles.},

  doi = {10.1111/mec.12089},

  file = {Gautier2012.pdf:Gautier2012.pdf:PDF},

  institution = {Inra, UMR CBGP (INRA - IRD - Cirad - Montpellier SupAgro), Campus

international de Baillarguet, CS 30016, F-34988, Montferrier-sur-Lez,

France.},

  language = {eng},

  medline-pst = {aheadofprint},

  owner = {Claudius},

  pmid = {23110526},

  timestamp = {2012.11.06},

  url = {http://dx.doi.org/10.1111/mec.12089}

}

and 

@ARTICLE{Luca2011,

  author = {Francesca Luca and Richard R Hudson and David B Witonsky and Anna

Di Rienzo},

  title = {A reduced representation approach to population genetic analyses

and applications to human evolution.},

  journal = {Genome Res},

  year = {2011},

  volume = {21},

  pages = {1087--1098},

  number = {7},

  month = {Jul},

  abstract = {Second-generation sequencing technologies allow surveys of sequence

variation on an unprecedented scale. However, despite the rapid decrease

in sequencing costs, collecting whole-genome sequence data on a population

scale is still prohibitive for many laboratories. We have implemented

an inexpensive, reduced representation protocol for preparing resequencing

targets, and we have developed the analytical tools necessary for

making population genetic inferences. This approach can be applied

to any species for which a draft or complete reference genome sequence

is available. The new tools we have developed include methods for

aligning reads, calling genotypes, and incorporating sample-specific

sequencing error rates in the estimate of evolutionary parameters.

When applied to 19 individuals from a total of 18 human populations,

our approach allowed sampling regions that are largely overlapping

across individuals and that are representative of the entire genome.

The resequencing data were used to test the serial founder model

of human dispersal and to estimate the time of the Out of Africa

migration. Our results also represent the first attempt to provide

a time frame for the colonization of Australia based on large-scale

resequencing data.},

  comment = {read; uses a RAD type genotyping protocol; presents an interesting

aproach to SNP calling using a coverage matrix; contains sophisticated

methods to correct for the bias in estimates of nucleotide diversity

due to allele drop out (i. e. null alleles due to polymorphisms in

the restriction sites)},

  doi = {10.1101/gr.119792.110},

  file = {Luca2011.pdf:Luca2011.pdf:PDF;:Luca2011supp.pdf:PDF},

  institution = {Department of Human Genetics, University of Chicago, Chicago, IL

60637, USA},

  keywords = {allele drop out,},

  language = {eng},

  medline-pst = {ppublish},

  owner = {Claudius},

  pii = {gr.119792.110},

  pmid = {21628451},

  timestamp = {2011.09.16},

  url = {http://dx.doi.org/10.1101/gr.119792.110}

}

claudius

--
You received this message because you are subscribed to the Google Groups "NGS Group APS Sheffield" group.
To unsubscribe from this group and stop receiving emails from it, send an email to NGSshef+u...@googlegroups.com.
To post to this group, send an email to NGS...@googlegroups.com.
Visit this group at http://groups.google.com/group/NGSshef?hl=en-GB.
For more options, visit https://groups.google.com/groups/opt_out.
 
 
<mec12276-sup-0001-FigS1-S7.docx><mec12276.pdf>

[Ludovic Duvaux]

Dear all

see below for paper that might interest many people:
http://mbe.oxfordjournals.org/content/30/8/1745.full

Cheers,
Ludo

--
******************************************************************
Ludovic Duvaux, Postdoctoral Research Associate

Department of Animal & Plant Sciences
Western Bank
University of Sheffield
Sheffield, S10 2TN
United Kingdom

Tel: +44 (0) 1142220112

******************************************************************

[Ludovic Duvaux]

Another paper than can interest some of you:
http://www.biomedcentral.com/1471-2164/14/542
Ludo