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Three mechanisms can produce long CDR-H3s: (i) longer VH, DH, or JH genes can be used preferentially, (ii) CDR-H3 can be lengthened by insertions induced by activation-induced cytidine deaminase [9], [53], and (iii) secondary rearrangement (or receptor editing or revision [54], [55]) can result in N and P additions at the N1 junction.
These assumptions are violated with data from GWA studies as (i) longer genes usually have more SNPs resulting in a higher probability of being sampled and (ii) overlapping genes are sampled in clusters (Holmans et al., 2009).
The sequential pulsed analysis is able to augment this first preliminary report through reanalysis using: (i) longer reads and (ii) paired-end (PE) reads as the sequencing run progresses.
These assumptions are violated in genome-wide association (GWA) studies since (i) longer genes typically have more single-nucleotide polymorphisms resulting in a higher probability of being sampled and (ii) overlapping genes are sampled in clusters.
Typically, if a smaller Wmax is used, there are two effects on the CB region annotations: (i) longer CB regions are broken up into shorter stretches (of up to approximately the size of Wmax); (ii) subsidiary mild biases that can only be detected with longer window sizes are not considered.
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