Low-pass whole genome sequencing is a cost-effective alternative to traditional genotyping arrays or whole genome sequencing for trait mapping. It provides increased power over arrays, especially in non-European populations, by allowing discovery of new and rare variants across the genome. While computational methods are needed to analyze low-pass sequencing data, simulations and empirical studies show high concordance between low-pass sequencing and genotyping arrays. With large sample sizes, low-pass sequencing can also discover extremely rare variants present in only a few copies.

1. Imputation and de novo variant discovery from
low-pass whole genome sequencing data for
cost-effective and scalable trait mapping
Joe Pickrell
@joe_pickrell | joe@gencove.com

2. WHOLE GENOME SEQUENCING EXOME SEQUENCING
What technology to use to measure genotypes?
SNP ARRAY
O ($1000)
PROS: comprehensive
CONS: expensive, often overkill
O ($100)
PROS: comprehensive in exons
CONS: completely misses non-
coding variations
O ($10)
PROS: cost-effective, well-tested
CONS: no new variant discovery
(e.g. rare or population-specific),
for cost-effectiveness overall
genome coverage suffers

3. LOW-PASS SEQUENCING
What technology to use to measure genotypes?
SNP ARRAY
O ($10)
Sequencing technologies allow for new
variant discovery, high discovery power
across the genome.
O ($10)
PROS: cost-effective, well-tested
CONS: no new variant discovery
(e.g. rare or population-specific),
for cost-effectiveness overall
genome coverage suffers
+ 💻 =

4. Shotgun sequence a human genome to (usually) 0.4x or 1x coverage, and
use computational methods to ‘fill in’ anything we missed.
What is low-pass sequencing?
INTUITION
0.4x coverage = one sequencing read at ~30M SNPs
Genotyping array = excellent measurement of 0.5M SNPs

5. Why now?
2018: nominal price/Mb of sequence is <$0.01
The challenging part of low-pass sequencing is not sequencing per se

6. 1. Cost of commercial library prep kits or outsourcing is higher
(sometimes considerably higher) than the cost of sequencing.
The challenges in low-pass sequencing are in sample
preparation and analysis
2. Going from a fastq file of low-pass sequences to genetic variant
calls is non-trivial and no standard software exists.

7. 1. Divide the 1000 Genomes dataset in two
How does imputation from low-pass sequencing compare to
imputation from arrays?
2. Simulate low-pass sequencing (or genotyping from a few
commonly-used commercial arrays) from one half, impute from
the other

8. In an African population, low-pass sequencing increases
effective power by ~50-100%

9. In a European population, low-pass sequencing increases
effective power by ~10-20%

10. How does imputation from low-pass
sequencing compare to imputation
from arrays?
Up to now this is all simulations.
What about in practice?

11. How does imputation from low-pass
sequencing compare to imputation
from arrays?
79 European-ancestry individuals sequenced to
~1x coverage
Downsampled to 0.4x, 0.6x, 0.8x
Genotyped on the Affymetrix Axiom Biobank
Precision Medicine Research Array, around 800k
SNPs
Collaboration with Charlie Cox, GSK

12. High concordance between
genotyping array and imputed low-
pass genome sequences
Concordance at non-reference genotypes at non-reference genotypes

13. Low-pass sequencing increases power relative to the
PMR array

14. Can low-pass sequencing be used
to discover variants?
Ignore genotype data, call variants
from the sequencing reads alone
What fraction of polymorphic
variants are identified?

15. Can low-pass sequencing be used to discover variants?
With 1x sequencing, variants
present in >10 copies are
discovered.
The absolute number of copies
of the variant is more relevant
then the frequency per se; in
massive samples could profile
extremely rare variants.

16. | Low-pass sequencing increases association power by 10-100%
compared to commonly-used genotyping arrays, particularly in
non-European populations
Summary
| Low-pass sequencing allows for discovery of new/rare
variants, particularly at large sample sizes
| Additional applications: combining low-pass sequencing with
exon capture allows for joint clinical assays of rare and common
variation

17. THANKS!
Tomaz Berisa
Kaja Wasik
Maria Vazquez
Charlie Cox
Dana Fraser
Karen King
Joe Pickrell | @joe_pickrell | joe@gencove.com