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The Vast Majority of GWAS Discoveries Can
be Made Without Large-scale Sequencing
Nearby genetic variants are correlated with each other.
Knowing the variants one position allows the nearby
variants to be inferred.
E.g. Fill in the blanks:
The q***k brown f*x jumps ov*r the **zy dog.
●
• The same principle applies in genetics. The process of
filling in the gaps is known as 'genotype imputation'.
Genotyped Samples
2
2
2? 2
0 1?2?2?011?? 2 0
1?2?1?1? 120??2?0
27272727121 27 0
12 12 12 13 ??? 2?0
022222220 21 22 2 1
27121
2
1
2 0
17070
2
1
0
Reference Genomes
0 0 1 0 1 1 1 0 0 1 1 1 1 1 1 0
1 1 1 1 1 1 1 0 0 1 0 0 1 1 1 0
1 1 1 1 1 0 1 0 0 1 0 0 0 1 0 1
0 000 1 1 0 0 1 1 1 1 1 1 0
1 1 1 0 1 1 0 0 1 1 1 0 1 1 1 0
0010111001 11110
1 1 1 1 1 0 1 0 0 1 0 0 0 1 0 1
11000 100
1 1 0 1 1 1 0
Imputation Process
0?1?1?1? 01 ? ? 1? 0
1?1?1?1? 011? ?1? 0
1?1?1?1? 010?? 1? 0
1?1?1?1? 1 1 1? ?1? 0
1?0?0?0?111? ?1? 0
0?1? 0?0? 1 1 1? ? 1 ? 0
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Imputed Samples
1
2 0
1 2 200
2 1
112220011 2 0
11201110120122 0
22222120121122 0
1110121012212220
0121212002111211
2 2 111 101
121 0 0 2 2 2
0
022
2 1
22 0
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