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With the last release of our the Search & Match Service, WMDA  introduces a new haplotype frequency set configuration to better serve all patients and provide increased accuracy when matching donors and cord blood units to patients. The Search & Match Service currently contains no ethnicity information for donors and therefore the new frequency sets will be calculated and based upon geographical and available data of the donors of an organisation. These frequency sets utilize high resolution typing results from organisations to extrapolate the haplotypes of the region or organisation. Thus, an organisation or geographical region must meet a minimum threshold of number of donors and availability of high resolution typing to build usable and valuable frequencies. For cord blood units. we will use the same sets that were determined in the donor populations.

The inclusion criteria aims to balance a high number of donors, the quality of the HLA types and the complexity of the haplotype frequency estimation. The number and HLA types of the loci that are included in the estimation can be independent of the loci of the haplotypes actually estimated if the quality of the former is appropriate.

5-locus Haplofrequency estimation was performed on all organisations/populations with at least 5000 donors in HLA-A, -B, -C and -DRB1 types in 90% high resolution. Organisations in the same country/within the same population are usually combined, e.g. AT-ABMDR (Austrian Bone Marrow Donors) and AT-Verein (Austria- Verein geben fur Lebel) but *not* for US-NMDP (general US population) and US-GOL (predominantly Ashkenazi Jews). The 90% criteria is based on the global frequency set and includes all allele codes whose top 90% cumulated allele frequencies are in high resolution.

The current global frequency set will continue to be used for donors of organisations if it is the best representation. The number of this frequency set is 999.

Below, you can find a figure how the haplotype frequency (HF) sets are assigned to the donors and cord blood units. The system first determines if both COUNTRY and ETHNICITY are provided. If yes, then it will check if an ethnicity specific set for this country exists. If the donor for example is coming from USA and has ethnicity HISA, then we do not have a specific set available. However, there is a more broad Hispanic HF set available (USA-HI) and this will then be used.

If there is no ethnicity available for the donor or no ethnicity specific HF set exists for that country, the system will check if a country specific HF set is available or if the country is part of one of the regional HF sets.

If no country specific HF set is available, the Search & Match Service will use the global consensus HF set.



Flowchart assigning a haplotype frequency (HF) set

In the table below, you can find the haplotype frequency set numbers and which countries/organisations were included as well as the total sample size. In the last part from the table we included regional sets, some country/ethnicity specific sets and the global consensus set.

The regional sets are defined as follows:

East Asia (eas): CN (CN+CN1), HK, TW, JP (Set number: 32)

Eastern Europe (eeu):AT (A+A2), CZ (CS+CS2), CY (CY+CY2), GR2, PL (PL3+PL5+PL6), TR (TRAN+TRIS+TRKK), BG, HU, HR, LT, MK, RU (R2+R4), RO, RS, SK, SI (Set number: 33)

South America (sam): AR, BR, UY (Set number: 34)





INPUT DATA

HF set number

(pop_id)

Determination date

Sample size

ISO country code

ION

Search & Match Service_Registry_codes

Old BMDW Registry codes

12017-04-2526,352AR5117

AR-INCUCAI

AR
22017-04-2521,709AT

2614

4961

AT-ABMDR

AT-Verein

A

A2

32017-04-2538,548AU + NZ

7748

8261

AU-ABMDR

NZ-NZBMDR

AUS

NZ

42017-04-2549,392

BE

4201

BE-MDPB

B
52017-04-2582,656BR8766

BR-REDOME

BR
62017-04-25214,836CA

5103

6912

CA-One Match

CA-HemaQuec

CND

CND3

72017-04-2589,533CH9341

CH-SBSC

CH
82017-04-25591,099CN + HK + TW

2197

6681

4070

3458

CN-CMDP

CN-Sunsh

HK-HKBMDR

TW-Tzu Chi

CN

CN1

HK

TW

92017-04-2527,230CY

4278

9751

CY-Par BMDR

CY-CBMDR

CY

CY2

102017-04-2536,878CZ

4753

5440

CZ-CSCR

CZ-CNMDR

CS

CS2

112017-04-256,273,693DE6939

DE-ZKRD

D
122017-04-2520,364DK

2015

7484

DK-DSCDW

DK-DSDE

DK

DK2

132017-04-2559,177ES7813

ES-REDMO

E(+E2)
142017-04-2517,377FI9738Fi-FSCRFI
152017-04-25173,541FR1804FR-FGMF
162017-04-251,050,556GB + IE

6354

1726

2731

9968

5590

GB-Anthony

GB-WBMDR

GB-BBMR

GB-DKMS

IE-IUBMR

GB

GB3

GB4

GB5

IRL

172017-04-2538,855GR

1461

GR-CBMDP

GR2

182017-04-25377,768IL

5239

4987

4068

IL-Hadassah

IL-Ezer Miz.

IL-SHBB

IL

IL2

IL3

192017-04-25208,655IN

8486

2824

4131

4596

IN-Datri

IN-GeneBand

IN-MDR

IN-BMST

IN2

IN3

IN4

IN5

202017-04-25150578IT7450

IT-IBMDR

I
212017-04-25129,272NL8139

NL-Matchis

NL
222017-04-2520,925NO7214

NO-NBMDR

N
232017-04-251,167,906PL

3918

5391

7414

PL-ALF

PL-Poltranspl

PL-DKMS

PL3

PL5

PL6

242017-04-25158,284PT7258

PT-Cedace

P
252017-04-2525,498SA8118

SA-SSCDR

SA
262017-04-2545,892SE5285

SE-Tobias

S
272017-04-2562,785SG3785

SG-BMDP

SG
282017-04-2540,149TH8362

TH-TSCDR

TH
292017-04-2532,572TR

3893

5509

3503

TR-TRAN

TR-TRIS

TR-TURKOK

TRAN

TRIS

TRKK

302017-04-254,068,326US3553

US-NMDP

USA1
312017-04-25163,588US1033

US-GOL

USA4
322017-04-25792,159CN+HK+TW+JP

eas

Search&Match:easCN+CN1+HK+TW+JP
332017-04-251,369,965

AT+CZ+CY+GR+PL+TR+BG+HU+

HR+LT+MK+RU+RO+RS+SK+SI

eeuSearch&Match:eeu

A+A2+CS+CS2+CY+CY2+GR+GR2+PL3+PL5+PL6+TRAN+

TRIS+TRKK+BG+H+HR+LT+MK+R2+R4+RO+RS+SK+SLO

342017-04-25109,841AR+BR+UYsamSearch&Match:samAR+BR+UY
1002016-09-30151,204DE-ASSW-DE-ASSW subsetDE-ASSW
1012017-04-05656,591US-AF (ZKRD)-

US-AF subset (ZKRD_estimation)

USA1-AF
1022017-04-05796,780US-AS (ZKRD)-US-AS subset (ZKRD_estimation)USA1-AS
1032017-04-053,740,668US-CA (ZKRD)-US-CA subset (ZKRD_estimation)USA1-CA
1042017-04-051,002,893US-HI (ZKRD)-US-HI subset (ZKRD_estimation)USA1-HI
9992015-12-1611,430,561

Global consensusAll Search & Match Service donor registries with a sufficient number of donors with the defined level of HLA typing.


Since WMDA is doing these calculations on behalf of organisations, it is important for organisations to submit high resolution typing when available and donor ethnicity data. This greatly improves the haplofrequency sets generated and allows for individual donor match grades to be more accurate. 


It is important to know that your organisations frequency set is changeable!

You can request that your donors be returned to the global consensus haplofrequency set or to a regional set. Your request should include the reasons why you believe that another set is more applicable for your donors. Additionally, if your organisation has a frequency set available that you would like to see utilized for the donors of your organisation we can implement it as well. In this case, your request should include at least a description about your population, the sample size, inclusion and exclusion criteria, calculation method, and the reasons why your haplofrequency set would be better than the current set applied by WMDA. Both requests will be reviewed by the WMDA BioInformatics Working Group. Please send requests to support@wmda.info . In the future, you'll be able to dictate a frequency set on a per donor basis. 


DateVersionDescriptionAuthor
2017-10-311.0Replacement BMDW global haplotype frequency set for more specific setsJK
2018-01-241.1Modification some sets; introduced during OptiMatch version 3.31.0JK
2019-02-151.2Replaced BMDW by WMDA / Search & Match Service; updated email addressJK
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1 Comment

  1. Dear Emma, 

    Thank you for this excellent summary. Two comments.

    "If is not enough data to calculate a geographical frequency set then the current global frequency set will continue to be used for a registry's donors."

    There are broad geographical frequency sets for Eastern Asia, Eastern Europe and South America.

    "Additionally, if your registry has frequency sets available that you would like to see utilized we can implement those as well."

    That is currently one frequency set per registry. In the future, your registry will be able to assign individual frequency sets to every donor.

     

    Cordially yours,

    Hans-Peter