Download Unravelling the genetic component of male infertility Alexandra Lopes

Unravelling the genetic component
of
male infertility
Alexandra Lopes
May 2015
Researcher @ Pop Genetics, i3S/IPATIMUP
Nov. 2011
Postdoc fellow @ Pop Genetics & Dep. Genetics, WUSTL, USA
May 2010
PI: “Search for genomic structural variants in azoospermia: a study in the
Portuguese population”, IPATIMUP
2007-2011
Postdoc fellow @ Pop Genetics & Mammalian Mol. Genetics lab
U. Cambridge, UK
2002 – 2006
PhD student @ Pop Genetics lab, IPATIMUP, PT
2001
Biology degree, FCUP, PT
X&Y
BIOLOGY
Nabeel Affara
Cambridge, UK
Lounes Chikhi
IGC
POPULATION
GENETICS
& EVOLUTION
CHR.
REARRANG.
João Alves
GABBA PhD
António
Amorim
IPATIMUP
Ana Lima Don Conrad
GABBA PhD
WUSTL
FUNCTIONAL
GENOMICS
EPIGENETICS
X-INACT.
Laura Carrel
Penn State
REPROD.
BIOLOGY
Catarina Seabra
UA MSc
Genetics of Male Infertility Initiative
(GEMINI)
International consortium to study the genetics of male infertility
Analysis of large number of patients by high density arrays and
exome sequencing
Genetics wiki
DNA
Human Chromosomes
Single base variant
Single Nucleotide Polymorphism (SNPs)
• Change a single DNA letter
• Most frequent genetic
variant
• 1 per 300 base pairs
• Common (MAF>5%)
• Less common (1-5%)
• Rare ‘variants’ (<1%)
•“SNV”
Genotypes
BB
or
AB
or
AA
Locus 4
Alleles at
locus 4
A
B
Each somatic cell is diploid
Locus: chromosomal location
that’s polymorphic.
Alleles: different variants @ locus
(two copies of each autosome)
Thus, 3 genotypes at locus 4
PAR 1
X
X and Y Chromosomes
Y
PAR 1 ~2.7 Mb
X chromosome:
~ 150 Mb
MSY
Usp9y
~ 1000 functionally diverse genes
Ross et al. (2005)
Y chromosome:
Male determining locus SRY
PAR 2 ~300 Kb
~ 23 Mb (coding region)
~ 156 transcripts; many multi-copy gene
families expressed in testis
Skaletsky et al. (2003)
PAR 2
B
Y chr
Alleles at A
B
locus
or
A
Genetics of male infertility
Human fertility facts
▪ As many as 8% of children in some Western countries
are born as a result of assisted reproductive techniques
▪ 1 out of 7 European couples suffer from reproductive
disorders resulting in infertility
▪ In 30-50% of the cases the male is the infertile partner
Known genetic causes of non-obstructive
azoospermia (NOA)
15%
15%
70%
?
Some sporadic mutations have been
associated with male infertility
ANEUPLOIDY
Y CHR DELS
UNKNOWN
Genetic architecture of
spermatogenic failure
Genetic architecture of a trait
• the number of genes/loci modulating the trait
• the number of risk alleles at each gene/locus
• their frequencies and effect sizes
Our Aim
To detect rare variants across the genome with
strong association with infertility
Approach
Genome-wide analysis in infertile patients
(azoospermic) to detect rare variants
single base variants (exome sequencing – NGS)
Previous Results
New generation sequencing era
New generation sequencing
(NGS) wiki
Benjamin Meder et al. Circ Cardiovasc Genet. 2011;4:110-122
Copyright © American Heart Association, Inc. All rights reserved.
Variant calling
NGS technologies have inherent
error – uncertainty in the data
Benjamin Meder et al. Circ Cardiovasc Genet. 2011;4:110-122
Copyright © American Heart Association, Inc. All rights reserved.
Genotypes
BB
or
AB
or
AA
Locus 4
Alleles at
locus 4
A
B
Each somatic cell is diploid
Locus: chromosomal location
that’s polymorphic.
Alleles: different variants @ locus
(two copies of each autosome)
Thus, 3 genotypes at locus 4
Assembly and mapping
Assembly and mapping depends on the quality
of the reference genome sequence
Association tests
Opportunities and challenges of
the analysis of sex chromosomes’
variants by NGS
Opportunities
1. Sex chromosomes are prime candidates for
variants involved in male reproduction – support
from previous results
2. Biological properties of the Y chr allow specific
strategies
Before eggs and sperm are formed mom and dad’s
chromosomes exchange information
DAD’s CHR
MOM’s CHR
our children will carry new combinations of alleles
Not on the Y chromosome!!!
Y chr is inherited in a block accumulating
mutations linearly with time
Zhang M, Wang CC, Yang C, Meng H, Agbagwa IO, et al. (2016) Epigenetic Pattern on the Human Y Chromosome Is Evolutionarily
Conserved. PLoS ONE 11(1): e0146402. doi:10.1371/journal.pone.0146402
http://journals.plos.org/plosone/article?id=info:doi/10.1371/journal.pone.0146402
A group of mutations defines
a haplogroup (lineage)
Well defined phylogeny (tree of related sequences)
Using haplogroup information to call new variants
Challenges
1. Variant calling
Y chr is hemizygous (one copy in males) – lower
signal-to-noise ratio
2. Variant filtering to eliminate false positives
3. Mismapping
- Y chr sequence is still incomplete and has many
repetitive regions
- Homology to X chr in some regions
Até 31 de Março 2016!!
Contactem-nos!!
Alexandra Lopes
[email protected]
Eduardo Sousa
UM/FCUP
[email protected]