ALFRED: allele frequency database
      The ALlele FREquency Database   
ALFRED is a resource of gene frequency data on human populations
supported by the Yale Center for Medical Informatics.

How we came to this conclusion
Proposed sites

ALFRED staff have recently analyzed the data in ALFRED and have come to an important conclusion. There is not a complete data set on a large number of populations with a significant number of polymorphic sites typed for those populations. This presents a problem for those in population genetics who want to do an integrated worldwide analysis. We believe this could be a great opportunity for the population genetics community to work together. One idea to combat this issue would be for researchers to focus on an agreed upon set of sites. To get a discussion going, we have put together a suggested set of polymorphic sites based on what is already found in ALFRED and what we know about ongoing research. If researchers can come together to address this problem, detailed definitions of population relationships could be assessed both worldwide and regionally.
How we came to this conclusion:
ALFRED staff has recently analyzed several data sets taken directly from ALFRED which led us to the above conclusion.
Data Set #1:
We wanted to include a number of sites typed for a large number of populations. In order to accomplish this we had to dramatically decrease the number of sites included. We identified five Alu- insertion/deletion polymorphic sites (ACE, PLAT, APOA1, CDH13 and F13B) typed for approximately 157 worldwide population samples. Any increase in numbers of sites resulted in many fewer populations with complete data. Because the number of sites is so small, the data on the population relationships was not clear.
Data Set #2:
Separately, we chose fifty markers scattered around the genome that had been typed for 38 separate worldwide populations (data provided by the lab of Dr. Kenneth Kidd, Yale University Medical School). The analysis showed a dramatic increase in the definition of the population relationships and provided a much clearer pattern of population distribution.
Proposed sites:
The following is the suggested list of polymorphic sites the ALFRED staff have put together to be typed in rank order (to ensure there will always be some sites in common for a large number of populations). This list should be looked at as a starting point for further discussion and would be amended accordingly.

Locus Symbol, Site (UID)Current # of Populations
F13B, FXIIIB Alu insertion (SI000799Z)128
CDH13, PV92 Alu insertion (SI000802K)166
APOA1, APO Alu insertion (SI000798Y)169
ACE, ACE Alu indel (SI000241H)199
PLAT, TPA25 Alu insertion (SI000152I)191
ALU-D1, D1 Alu insertion (SI000800I)120
CD4, Alu Ins/Del (SI000128L)85
CHORDC1, B65 Alu insertion (SI000701I)91
ALU-A25, A25 Alu insertion (SI000801J)74
ALU-HS4.65, HS4.65 Alu insertion (SI000825P)79
ALU-HS2.43, HS2.43 Alu insertion (SI000822M)74
ALU-HS4.32, HS4.32 Alu insertion (SI000824O)64
ALU-HS4.75, HS4.75 Alu insertion (SI000826Q)63
COL3A1, COL3A1 Alu insertion (SI000820K)61
ALU-HS4.14, HS4.14 Alu insertion (SI000821L)60
Additional RFLP sites:
The following loci and sites have been suggested because of not only is already in ALFRED but the ongoing research in several laboratories.
Locus Symbol Site (UID)Current # of Populations
ANKK1 TaqI A (SI000144J)68
DRD2 intron 1 TaqI B (SI000148N)109
intron 2 TaqI D (SI000139N)62
ADH1B intron3 RsaI (SI000002C)91
exon3 Arg48His (SI000229N)247
exon9 Arg370Cys (SI000230F)94
ADH1C exon 5 HaeIII (SI000227L)75
exon 8 Ile350Val (SI000228M)136
intron 2 EcoRI (SI000226K)48
ADH7 intron 6 StyI (SI000231G)82

Other genes/sites studied on many populations:
HBB-Beta hemoglobin sites and haplotypes
PAH-Phenylalanine Hydroxylase
     Particularly BglII, PvuII A, MspI and XmnI
APOB-Apolipoprotein B
HOXB-Homeo Box B gene cluster
     Particularly HOXB4-MspI

© 2019 Kenneth K Kidd, Yale University. All rights reserved. The full Copyright Notification is also available.
Originally prototyped by Michael Osier with the aid of Kei Cheung
Upgrades and maintenance since 2002 by Haseena Rajeevan