Analysis of meiotic recombination in 22q11.2, a region that frequently undergoes deletions and duplications

Torres-Juan, Laura; Rosell, Jordi; Sánchez-de-la-Torre, Manuel; Fibla, Joan; Heine-Suñer, Damià

doi:10.1186/1471-2350-8-14

BMC Medical Genetics

Table 2 Descriptive data used for the analysis of the Hapmap population-based recombination profile of the 22q11.2 region

From: Analysis of meiotic recombination in 22q11.2, a region that frequently undergoes deletions and duplications

Characteristics of windows							General model for recombination (MR0) ⁽¹⁾	Simple hotspot model for recombination (MR1) ⁽²⁾
	Chromosome position								Hotspot boundaries ⁽⁴⁾ (chromosome position)				Bayes factor (BF)⁽⁶⁾ (log BF)
Window	begin	end	Window length (bp)	SNPs/window	SNP density (bp/SNP)	LCR containing windows	Population recombination rate (ρ/bp ⁽³⁾	Population recombination rate (ρ/bp ⁽³⁾	left	rigth	Hotspot width (bp)	Hotspot Intensity ⁽⁵⁾ (λ)	λ > 10	λ > 100
I	16000790	16396314	395524	126	3139		0.00079688	0.00139749	16192800	16198100	5300	200(70:438)	3.00	0.59
II	16402210	16801972	399762	187	2138		0.00028288	0.00053267	16683800	16691200	7400	28.2(1.2:145)	-0.03	-1.13
III	16802997	17601177	798180	275	2902	LCR22-2	0.00020637	0.00044908	17111470	17296800	185330 (*LCR22-2*)	298(66:955)	3.00	1.05
IV	17603290	17998020	394730	137	2881		0.00004115	0.00007356	17963500	17971900	8400	762(466:990)	3.00	3.00
V	18006919	18406881	399962	157	2548		0.00039653	0.00076869	18032000	18041400	9400	42(1.8:145)	0.21	-1.00
VI	18414421	19205939	791518	173	4575	LCR22-3A	0.00025670	0.00058289	18737180	18897600	160420 (*LCR22-3A*)	147(12:805)	1.67	-0.38
VII	19215813	19613455	397642	141	2820	LCR22-3B	0.00010245	0.00030662	19229800	19237700	7900	2,6(1:8)	1.45	-3.00
VIII	19624609	20406127	781518	158	4946	LCR22-4	0.00036461	0.00068812	19947500	20081300	133800 (*LCR22-4*)	188(10:903)	1.26	-0.43
IX	20435862	20835601	399739	129	3099		0.00015527	0.00029812	20634600	20640300	5700	8,5(1,15:32,5)	-0.54	-2.70
X	20835924	21235614	399690	81	4934		0.00061587	0.00068451	20881700	20885700	4000	131(417:307)	3.00	0.09
XI	21238221	21625884	387663	68	5701	LCR22-5	0.00051035	0.00087814	21432500	21439900	7400	370(9:890)	1.24	0.39
XII	21640460	22037074	396614	139	2853		0.00007681	0.00018216	21668195	21676200	8005	6(1.1:19)	-0.78	-3.00
XIII	22040766	22438098	397332	97	4096		0.00042922	0.00052211	22247500	22250300	2800	702(391:966)	3.00	3.00
XIV	22441140	22840845	399705	124	3223	LCR22-6	0.00010236	0.00013618	22514100	22519600	5500	447(211:780)	3.00	2.22
XV	22844929	23194681	349752	82	4265		0.00002937	0.00002733	23002500	23014000	11500	480(130:898)	3.00	1.63
Total region	16000790	23194681	7193891	2074	3469		0.000290	0.000516

(1) Background population recombination rate (ρ) was estimated for each window using genotype data available at the HAPMAP project for CEU unrelated individuals, genotypes were analyzed by the PHASE v2.1.1 software using the general model for recombination rate variation (-MR0 option) after performing 1.000 iterations to estimate posterior distribution of recombination parameters (-X10 option). All the analyses were performed running PHASE five times and selecting the best average value for the "goodness of fit" (-x5 option). We computed all the recombination parameters estimates based on the recombination output file, which provides a sample from the posterior distribution of the background recombination rate (ρ) per base pair and the factor by which the recombination rate between two adjacent SNPs exceeds the background rate (λ).
(2) The presence of a recombination spot was estimated for each window by the PHASE v2.1.1 software using the simple hotspot model for recombination (-MR1 option) after performing 1000 iterations to estimate posterior distribution of recombination parameters (-X10 option), We computed all the recombination parameters estimates based on the hotspot output file, which provides a sample from the posterior distribution of the background recombination rate (ρ) per base pair, the factor by which the recombination rate in the hotspot exceeds the background rate (λ) and the left and right ends of the hotspot.
(3) From the estimated recombination parameters we computed the median ρ of each window and the median ρ of the 22q11.2 region by a weighted average of the median ρ of each window.
(4) Hotspot boundaries were considered to extend from the 5th percentile of the posterior probability for the left end to the 95th percentile for the right end.
(5) Of the 1.000 draws from the posterior distribution of λ we computed the median and the 5th and 95th percentile.
(6) From the posterior distribution of λ, we computed the probability of both: λ > 10 and λ > 100 and computed the associated Bayes Factor (BF) to asses the statistical support of a recombination spot. A BF > 10 (Log BF > 1) was taken to indicate the presence of a recombination spot, that was considered as a warm spot if BF > 10 (Log BF > 1) computed under P(λ > 10) and hotspot if BF > 10 (Log BF > 1) computed under P(λ > 100).

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ISSN: 1471-2350

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