Table 3 Chromosome regions highlighted by linkage analysis

From: Genome-wide analysis of genetic susceptibility to language impairment in an isolated Chilean population

Chr

Max rec HLOD

SNP (chr posn) of max rec HLOD

Max dom HLOD

SNP (chr posn) of max dom HLOD

CEPH max NPL score (P-value)

SNP (chr posn) of max CEPH NPL score

Founder max NPL score (P-value)

SNP (chr posn) of max founder NPL score

All max NPL score (P-value)

SNP (chr posn) of max all NPL score

No. Homo Runs

 1

1.23

rs2129975 (92054668)

    

1.26 (0.10)

rs792321–rs481387 (74454556–74483038)

  

1

 1

1.52

rs1906255 (186438670)

    

1.05 (0.15)

rs2039759 (191870092)

   

 2

    

3.90 (5.0 × 10−5)

rs3102960 (8369948)

2.63 (0.004)

rs2001660 (9530892)

2.37 (0.009)

rs2001660 (9530892)

 

 4

  

1.03

rs11098966 (129566420)

      

1

 5

  

1.15

rs1553578 (40704941)

       

 5

  

1.15

rs1200485 (72420814)

      

1

 5

  

1.74

rs270664 (158489316)

      

1

 6

1.25

rs6926835 (12335531)

  

3.96 (4.0 × 10−5)

rs761116 (9566315)

3.23 (0.0006)

rs761116 (9566315)

1.96 (0.03)

rs2876143 (8928623)

1

 6

  

1.65

rs880900 (167059469)

7.56 (3.2 × 10−14)

rs927450–rs675162 (160102086–160696315)

    

1

 7

1.24

rs1476640-rs768055 (141058779–141059520)

  

6.73 (4.0 × 10−11)

rs1524341–rs1024676 (146337622–146346794)

6.10 (9.9 × 10−10)

rs1524341–rs1024676 (146337622–146346794)

6.00 (9.9 × 10−10)

rs928916–rs969356 (141954283–143804256)

2

 8

  

2.40

rs1390950 (11633238)

      

3

 8

  

1.88

rs749540 (41600253)

      

1

 8

    

3.95 (4.0 × 10−5)

rs268564 (71646063)

     

 8

1.09

rs1353277 (116148616)

1.28

rs727581 (116719666)

       

 8

    

3.69 (0.0001)

rs1375062–rs768803 (142034963–143203532)

3.04 (0.0013)

rs1868280–rs1375062 (141965436–142034963)

2.59 (0.005)

rs4246828–rs9071 (144240466–145721314)

 

 9

    

3.72 (0.0001)

rs717081 (20277139)

3.61 (0.0002)

rs1532310–rs1532309 (592986–593192)

1.21 (0.11)

rs263580 (17029312)

 

11

  

1.27

rs1945906 (81238725)

       

11

1.20

rs3345 (131346779)

1.16

rs2044727 (131644201)

1.44 (0.08)

rs3345 131346779

1.25 (0.10)

rs3345 (131346779)

   

12

    

1.13 (0.13)

rs937538–rs7960480 (132120315–132288239)

6.14 (9.9 × 10−10)

rs595241–rs632610 (132164652–132170791)

   

13

1.01

rs1572372-rs3847993 (19738004–20193194)

         

13

    

4.78 (8.0 × 10−7)

rs980285 (37937932)

2.66 (0.004)

rs980285 (37937932)

1.89 (0.03)

rs1544295 (42396689)

2

13

1.04

rs2044348 (88700438)

  

3.49 (0.0002)

rs996297–rs979969 (84905498–87095102)

3.47 (0.0003)

rs407218–rs979969 (85344625–87095102)

3.43 (0.0003)

rs407218–rs979969 (85344625–87095102)

 

14

1.04

rs961700-rs1015023 (67401190–67431984)

         

15

1.05

rs1557874 (23139577)

  

1.57 (0.06)

rs2596156 (31529470)

1.42 (0.08)

rs2596156 (31529470)

1.25 (0.11)

rs2596156 (31529470)

4

17

  

1.04

rs2215054 (12779734)

       

17

    

4.49 (3.0 × 10−6)

rs1046875–rs1046896 (78278715–78278822)

3.26 (0.0006)

rs1046875–rs1046896 (78278715–78278822)

1.31 (0.10)

rs1046875–rs1046896 (78278715–78278822)

1

22

1.00

rs1540297 (34440411)

         
  1. Abbreviations: Chr, chromosome; posn, position; max, maximum; SNP, single nucleotide polymorphism.
  2. Results are given for any region that achieved a genome-wide suggestive NPL score>3.8 (P=0.0007) or a parametric HLOD>1. Information is also given regarding any homozygous stretches identified in linkage regions (No. Homo Runs). The positions of homozygous tracts are given in Table 2.
  3. Non-parametric linkage analyses were completed using: (i) the CEPH allele frequencies (CEPH columns), (ii) allele frequencies calculated from the genotype data of the founder members (founder columns) and (iii) allele frequencies calculated from the all genotyped individuals (All columns). Only NPL-scores of greater than 1.0 are reported.
  4. Parametric linkage analyses were completed under a dominant (dom) and recessive (rec) model. Only HLOD scores>1.0 are reported.
Back to article page