A collection of reference arrays was made with them.
IMPUTE explicitly specifies a set of reference haplotypes (e.g., haplotypes from the HapMap project), as the pool of hidden states of the Markov Chain, and infers haplotypes and missing genotypes in test samples according to these hidden states [5].
For population P, simulate a cohort of 1,000 individuals by selecting pairs of reference haplotypes, at random, from HMP3.
Whereas the original algorithm imputes genotypes from the full set of reference haplotypes, the new approximation imputes each study haplotype from a custom subset of reference haplotypes.
Our method can also use existing panels of reference haplotypes.
The algorithm for computing the haplotype connectivity of a collection of haplotypes can handle collections of several hundred haplotypes without difficulty.
We describe how the haplotype connectivity for a collection of haplotypes can be computed efficiently and briefly discuss some related optimization problems that arise in this context.
ACE ('Assessing Changes to Exons') converts phased genotype calls to a collection of explicit haplotype sequences, maps transcript annotations onto them, detects gene-structure changes and their possible repercussions, and identifies several classes of possible loss of function.
Microsoft releases Microsoft Bookshelf, a collection of ten popular reference publications.
The NCBI RefSeq database is a curated, non-redundant collection of reference sequences for each organism [ 26].
To further confirm the effect of the haplotype on gene expression, we examined the haplotype-based eQTL in a collection of 462 benign prostate tissues and observed haplotype-dependent dosage effect on ASCL2 expression with two copies of A A A showing the highest gene expression (P = 2.65E−06) (Fig. 5d).
