LD was obtained from a local TCM practitioner (London, UK).
However, a clear advantage of our hydroponic system is that plants grow faster: synchronous induction can be achieved with 6- or 7-week old non-vernalized plants, while the floral induction of 8-week old plants by a single LD was obtained on soil, only if the seeds had been previously vernalized for several weeks.
The results of LAMP-LD were obtained with default parameters.
Low LDs were obtained as well for env genes located on the same chromosome, i.e. for HERV-F(c 2, HERV-K2, HERV-R, HERV-W (on chromosome 7) and for HERV-H1 and HERV-H3 (on chromosome 2; 10 Mb apart).
Higher resolution images of LDs are obtained by electron microscopy and electron tomography (Binns et al. 2006; Perktold et al. 2007; Czabany et al. 2008; Jacquier et al. 2011; Wolinski et al. 2011), which also demonstrate their close physical interactions with other intracellular organelles, in particular the ER, mitochondria, and peroxisomes (Binns et al. 2006; Pu et al. 2011).
LD data were obtained from HapMap (Release #27, NCBI 36, CEU) and lifted over to GRCh37/hg19.
Estimates of pairwise linkage disequilibrium (LD) values (D') were obtained using the HaploView software (version 4.2).
Haplotype frequencies and linkage disequilibrium (LD) measurements were obtained using SHEsis Software (online version: http://analysis.bio-x.cn/SHEsisMain.htm) based on the observed genotypes.
In addition, to ensure that sufficient SNP pairwise comparisons are available to obtain estimates of r 2 with acceptable precision, we used a maximum distance between SNPs of 15 Mb (from which 180 LD measures were obtained), which translated into 5 generations in the past.
Distributions of demographic and clinical variables were compared between patients and controls using chi-square tests or t-tests, and estimates of pair-wise LD between SNPs were obtained using Haploview software, version 4.1 [30].
LD data and gene information were obtained with the SNAP tool [ 78].
