[an error occurred while processing this directive]
On this page:
 

Measuring Haplotype Rarity

This appendix is to illustrate calculation methods for determining haplotype scores. We will not reprise the >300,000 calculations.

Appendix E: Calculation Examples

The examples here are for 37 markers. Markers >#37 would be scored by similar methods.

Marker Score Calculations

Prior to scoring a haplotype, a score for each marker's allele value was determined. Let us take DYS570 in Haplotype 1 to illustrate:

For the study these calculations were performed in an Excel spreadsheet, using indexing formulas, e.g., for this haplotype:

In most instances, the haplotype will contain modal values for most markers. Marker scores with modal values will evaluate to

Haplotype 1: Very Common

This haplotype matches the WAMH for 12 markers and differs significantly from R1b modals in only four of the 37 markers given here.

 Total Score 12 33.14 566.1 789 101112
DYS 393DYS 390DYS 19DYS 19bDYS 391DYS 385aDYS 385bDYS 385cDYS 426DYS 388DYS 439DYS 389iDYS 392DYS 389ii
Alleles13 2414 111114 1212 121313 29
Wheaton 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Ratio 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Deviation 0 0 0 0 * 0 0 0 0 0 0 0 0 0 0
STR 131415 161718 192021 222324 2525.1
DYS 458DYS 459aDYS 459bDYS 455DYS 454DYS 447DYS 437DYS 448DYS 449DYS 464aDYS 464bDYS 464cDYS 464dDYS 464efg
Alleles179 101111 241519 291415 1617
Wheaton 126 0 0 0 0 0 52 0 0 0 65 0 9 0 0
Ratio 1.18 1 1 1 1 1 2.68 1 1 1 4.25 1 1.17 1 1
Deviation 1.52 0 0 0 0 0 20 0 0 0 13 0 4.6 0 0
STR 262728 293031 323334 353637  
DYS 460GATA-H4YCA IIaYCA IIbDYS 456 DYS 607DYS 576DYS 570CDYaCDYbDYS 442DYS 438
Alleles1011 192316 151813 363712 12
Wheaton 248 55 0 0 0 0 0 0 56.6 0 10 0 0
Ratio 1.22 3.12 1 1 1 1 1 1 2.32 1 1.14 1 1
Deviation 3.18 0.246 0 0 0 0 0 0 59.7 0 20 0 0

Haplotype 2: Average

This haplotype significantly departs from R1b modal in eight markers

<
 Total Score1 233.1 456 6.178 91011 12
DYS 393DYS 390DYS 19DYS 19bDYS 391DYS 385aDYS 385bDYS 385cDYS 426DYS 388DYS 439DYS 389iDYS 392DYS 389ii
Alleles13 2314 111114 1212 111413 29
Wheaton 143 0 38 0 0 0 0 0 0 0 0 39 66 0 0
Ratio 1.38 1 1.95 1 1 1 1 1 1 1 1 2 4.3 1 1
Devn 14.07 0 110 0 * 0 0 0 0 0 20.4 38 0 0
STR13 141516 171819 202122 232425 25.1
DYS 458DYS 459aDYS 459bDYS 455DYS 454DYS 447DYS 437DYS 448DYS 449DYS 464aDYS 464bDYS 464cDYS 464dDYS 464efg
Alleles16 91011 112515 203015 161618
Wheaton 362 32 0 0 0 0 0 0 73 9 0 47 9 49 *
Ratio 1.47 1.64 1 1 1 1 1 1 4.32 1.15 1 2.62 1.17 2.58 *
Devn 11.25 25 0 0 0 0 0 0 53.2 7.39 0 10.2 4.6 12 *
STR 26 272829 303132 333435 3637  
DYS 460GATA-H4YCA IIaYCA IIbDYS 456DYS 607DYS 576DYS 570CDYaCDYbDYS 442DYS 438
Alleles10 111923 161518 173638 1212
Wheaton 417 55 0 0 0 0 0 0 0 0 0 0 0
Ratio 1.38 3.12 1 1 1 1 1 1 1 1 1 1 1
Devn 7.61 0.25 0 0 0 0 0 0 0 0 0 0 0

Haplotype 3: Uncommon

This haplotype has 15 markers departing significantly from R1b modals

 Total Score1 233.1 456 6.178 91011 12
  DYS 393DYS 390DYS 19 DYS 19bDYS 391DYS 385a DYS 385bDYS 385cDYS 426 DYS 388DYS 439DYS 389i DYS 392DYS 389ii
Alleles13 2414 101014 1212 121214 28
Wheaton 326 0 0 0 0 38 84 0 0 0 0 0 75 75 54
Ratio 2.3 1 1 1 1 2.15 7.46 1 1 1 1 1 4.75 6.36 2.46
Deviation 12.35 0 0 0 0 15 15 0 0 0 0 38 72 7.43
STR 131415 161718 192021 222324 2525.1
DYS 458DYS 459aDYS 459bDYS 455DYS 454DYS 447DYS 437DYS 448DYS 449DYS 464aDYS 464bDYS 464cDYS 464dDYS 464efg
Alleles1810 101211 241418 281515 1616
Wheaton 830 28 93 0 96 0 52 73 62 30 0 0 9 61 *
Ratio 4.01 1.56 19.6 1 33 1 2.68 5.87 3.82 1.51 1 1 1.17 2.97 *
Deviation 17.9 25 124 0 30.2 0 20 22.2 53.2 7.39 0 0 4.6 12 *
STR 2627 28 2930 31 3233 34 3536 37  
DYS 460GATA-H4YCA IIaYCA IIbDYS 456DYS 607DYS 576DYS 570CDYaCDYbDYS 442DYS 438
Alleles9 101923 161518 183639 1212
Wheaton 1,001 73.6 51 0 0 0 0 0 37 0 9 0 0
Ratio 3.23 3.83 2.76 1 1 1 1 1 1.86 1 1.13 1 1
Deviation 16.06 0.49 111 0 0 0 0 0 14.9 0 20 0 0

Measurement Tool

Download a tool to measure a single haplotype here.