12 research outputs found
First ancient mitochondrial human genome from a prepastoralist Southern African
The
oldest
contemporary
human
mitochondrial
lineages
arose
in
Africa.
The
earliest
divergent
extant
maternal
offshoot,
namely
haplogroup
L0d,
is
represented
by
click-‐speaking
forager
peoples
of
Southern
Africa.
Broadly
defined
as
Khoesan,
contemporary
Khoesan
are
today
largely
restricted
to
the
semi-‐
desert
regions
of
Namibia
and
Botswana,
while
archeological,
historical
and
genetic
evidence
promotes
a
once
broader
southerly
dispersal
of
click-‐speaking
peoples
including
southward
migrating
pastoralists
and
indigenous
marine-‐foragers.
Today
extinct,
no
genetic
data
has
been
recovered
from
the
indigenous
peoples
that
once
sustained
life
along
the
southern
coastal
waters
of
Africa
pre-‐pastoral
arrival.
In
this
study
we
generate
a
complete
mitochondrial
genome
from
a
2,330
year
old
male
skeleton,
confirmed
via
osteological
and
archeological
analysis
as
practicing
a
marine-‐based
forager
existence.
The
ancient
mtDNA
represents
a
new
L0d2c
lineage
(L0d2c1c)
that
is
today,
unlike
its
Khoe-‐language
based
sister-‐
clades
(L0d2c1a
and
L0d2c1b)
most
closely
related
to
contemporary
indigenous
San-‐speakers
(specifically
Ju).
Providing
the
first
genomic
evidence
that
pre-‐pastoral
Southern
African
marine
foragers
carried
the
earliest
diverged
maternal
modern
human
lineages,
this
study
emphasizes
the
significance
of
Southern
African
archeological
remains
in
defining
early
modern
human
origins.J. Craig Venter Family Foundation, La Jolla, CA, U.S.A. and the Max Planck Society (within
the laboratory of Svante Pääbo).http://gbe.oxfordjournals.orghb201
Next generation mapping reveals novel large genomic rearrangements in prostate cancer
Complex genomic rearrangements are common molecular events driving prostate
carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting
the full range and subtypes of large structural variants (SVs), greater than one
kilobase in length, is challenging using clinically feasible next generation sequencing
(NGS) technologies. Next generation mapping (NGM) is a new technology that allows
for the interrogation of megabase length DNA molecules outside the detection range
of single-base resolution NGS. In this study, we sought to determine the feasibility
of using the Irys (Bionano Genomics Inc.) nanochannel NGM technology to generate
whole genome maps of a primary prostate tumor and matched blood from a Gleason
score 7 (4 + 3), ETS-fusion negative prostate cancer patient. With an effective mapped
coverage of 35X and sequence coverage of 60X, and an estimated 43% tumor purity,
we identified 85 large somatic structural rearrangements and 6,172 smaller somatic
variants, respectively. The vast majority of the large SVs (89%), of which 73%
are insertions, were not detectable ab initio using high-coverage short-read NGS.
However, guided manual inspection of single NGS reads and de novo assembled
scaffolds of NGM-derived candidate regions allowed for confirmation of 94% of
these large SVs, with over a third impacting genes with oncogenic potential. From
this single-patient study, the first cancer study to integrate NGS and NGM data, we
hypothesise that there exists a novel spectrum of large genomic rearrangements in
prostate cancer, that these large genomic rearrangements are likely early events in
tumorigenesis, and they have potential to enhance taxonomy.This work was supported by Movember
Australia and the Prostate Cancer Foundation Australia
(PCFA) as part of the Movember Revolutionary Team
Award (MRTA) to the Garvan Institute of Medical
Research program on prostate cancer bone metastasis
(ProMis to P.I.C. and V.M.H.) dedicated to establishing
NGM for clinically relevant prostate cancer, and the
Australian Prostate Cancer Research Centre NSW
(APCRC-NSW). Participant recruitment and sampling
was supported by the Cancer Association of South Africa
(CANSA to M.S.R.B and V.M.H.). W.J. is supported by
APCRC-NSW, E.K.F.C. and D.C.P. are partly supported
by ProMis, P.I.C. is supported by Mrs Janice Gibson
and the Ernest Heine Family Foundation, Australia,
and V.M.H. is supported by the University of Sydney
Foundation and Petre Foundation, Australia.www.impactjournals.com/oncotargetam2018School of Health Systems and Public Health (SHSPH
The Australian dingo is an early offshoot of modern breed dogs
Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo
Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers
ADDITIONAL FILE 1: FIGURE S1. Concordant SV call generation from Manta
and GRIDSS. FIGURE S2. Summary of SVs in each type, compared to other
studies. FIGURE S3. CIRCOS plot of hyper-SV mutated tumours. FIGURE S4. The spread of SV breakpoints and samples in each 1 Mbp genomic bin. FIGURE S5. TMPRSS2-ERG fusion with interstitial region retention.
TABLE S1. Clinical and pathological characteristics of 180 prostate cancer
patients included in this study. TABLE S2. Biallelic assessment of CDK12
in hyper-duplicated samples. TABLE S3. Biallelic assessment of BRCA2 in
hyper-deleted samples.ADDITIONAL FILE 2: TABLE S4. Summary of gene fusions identified from SVs.
ADDITIONAL FILE 3: TABLE S5. SV calls resulting in gene fusions.DATA AND MATERIALS AVAILABILITY : The datasets analysed in this study were obtained and accessible through
Jaratlerdsiri et al [6], with sequence data deposited in the European GenomePhenome Archive (EGA; https://ega-archive.org) under overarching accession
EGAS00001006425 and including the Southern African Prostate Cancer Study
(SAPCS) Dataset (EGAD00001009067) and Garvan/St Vincent’s Prostate Cancer
Database (EGAD00001009066). The computational code used to analyse SV
subtypes, SV hotspots and gene fusions is available on GitHub [68].BACKGROUND : African ancestry is a significant risk factor for advanced prostate cancer (PCa). Mortality rates in sub-
Saharan Africa are 2.5-fold greater than global averages. However, the region has largely been excluded from the
benefits of whole genome interrogation studies. Additionally, while structural variation (SV) is highly prevalent, PCa
genomic studies are still biased towards small variant interrogation.
METHODS : Using whole genome sequencing and best practice workflows, we performed a comprehensive analysis
of SVs for 180 (predominantly Gleason score ≥ 8) prostate tumours derived from 115 African, 61 European and four
ancestrally admixed patients. We investigated the landscape and relationship of somatic SVs in driving ethnic disparity
(African versus European), with a focus on African men from southern Africa.
RESULTS : Duplication events showed the greatest ethnic disparity, with a 1.6- (relative frequency) to 2.5-fold (count)
increase in African-derived tumours. Furthermore, we found duplication events to be associated with CDK12 inactivation
and MYC copy number gain, and deletion events associated with SPOP mutation. Overall, African-derived
tumours were 2-fold more likely to present with a hyper-SV subtype. In addition to hyper-duplication and deletion
subtypes, we describe a new hyper-translocation subtype. While we confirm a lower TMPRSS2-ERG fusion-positive rate
in tumours from African cases (10% versus 33%), novel African-specific PCa ETS family member and TMPRSS2 fusion
partners were identified, including LINC01525, FBXO7, GTF3C2, NTNG1 and YPEL5. Notably, we found 74 somatic SV
hotspots impacting 18 new candidate driver genes, with CADM2, LSAMP, PTPRD, PDE4D and PACRG having therapeutic
implications for African patients.
CONCLUSIONS : In this first African-inclusive SV study for high-risk PCa, we demonstrate the power of SV interrogation
for the identification of novel subtypes, oncogenic drivers and therapeutic targets. Identifying a novel spectrum of SVs
in tumours derived from African patients provides a mechanism that may contribute, at least in part, to the observed
ethnic disparity in advanced PCa presentation in men of African ancestry.The Medical Health and Medical Research Council (NHMRC) of Australia, University of Sydney Bridging Grant, the USA. Department of Defense (DoD) Prostate Cancer Research Program (PCRP) Idea Development.https://genomemedicine.biomedcentral.comam2023School of Health Systems and Public Health (SHSPH
African-specific molecular taxonomy of prostate cancer
Data availability
DNA-sequencing data have been deposited at the European Genome-
Phenome Archive (EGA) under overarching accession EGAS00001006425
and including the Southern African Prostate Cancer Study (SAPCS)
Dataset (EGAD00001009067 and Garvan/St Vincent’s Prostate Cancer
Database EGAD00001009066). Academic researchers meeting the
data-access policy criteria may apply for data access through the
respective data access committees. CPGEA data are available through
http://www.cpgea.com. PCAWG data are available at ICGC Data Portal
(https://dcc.icgc.org/releases/PCAWG).Prostate cancer is characterized by considerable geo-ethnic disparity. African ancestry is a significant risk factor, with mortality rates across sub-Saharan Africa of 2.7-fold higher than global averages. The contributing genetic and non-genetic factors, and associated mutational processes, are unknown. Here, through whole-genome sequencing of treatment-naive prostate cancer samples from 183 ancestrally (African versus European) and globally distinct patients, we generate a large cancer genomics resource for sub-Saharan Africa, identifying around 2 million somatic variants. Significant African-ancestry-specific findings include an elevated tumour mutational burden, increased percentage of genome alteration, a greater number of predicted damaging mutations and a higher total of mutational signatures, and the driver genes NCOA2, STK19, DDX11L1, PCAT1 and SETBP1. Examining all somatic mutational types, we describe a molecular taxonomy for prostate cancer differentiated by ancestry and defined as global mutational subtypes (GMS). By further including Chinese Asian data, we confirm that GMS-B (copy-number gain) and GMS-D (mutationally noisy) are specific to African populations, GMS-A (mutationally quiet) is universal (all ethnicities) and the African–European-restricted subtype GMS-C (copy-number losses) predicts poor clinical outcomes. In addition to the clinical benefit of including individuals of African ancestry, our GMS subtypes reveal different evolutionary trajectories and mutational processes suggesting that both common genetic and environmental factors contribute to the disparity between ethnicities. Analogous to gene–environment interaction—defined here as a different effect of an environmental surrounding in people with different ancestries or vice versa—we anticipate that GMS subtypes act as a proxy for intrinsic and extrinsic mutational processes in cancers, promoting global inclusion in landmark studies.The National Health and Medical Research Council (NHMRC) of Australia, NHMRC Ideas Grants, University of Sydney Bridging Grant, the US Department of Defense (DoD) Prostate Cancer Research Program (PCRP) Idea Development Award TARGET Africa.http://www.nature.com/natuream2023School of Health Systems and Public Health (SHSPH
Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks
Motivation: We present PCIT, an algorithm for the reconstruction of gene co-expression networks (GCN) that combines the concept partial correlation coefficient with information theory to identify significant gene to gene associations defining edges in the reconstruction of GCN. The properties of PCIT are examined in the context of the topology of the reconstructed network including connectivity structure, clustering coefficient and sensitivity. Results: We apply PCIT to a series of simulated datasets with varying levels of complexity in terms of number of genes and experimental conditions, as well as to three real datasets. Results show that, as opposed to the constant cutoff approach commonly used in the literature, the PCIT algorithm can identify and allow for more moderate, yet not less significant, estimates of correlation (r) to still establish a connection in the GCN. We show that PCIT is more sensitive than established methods and capable of detecting functionally validated gene-gene interactions coming from absolute r values as low as 0.3. These bona fide associations, which often relate to genes with low variation in expression patterns, are beyond the detection limits of conventional fixed-threshold methods, and would be overlooked by studies relying on those methods
The Genetic Architecture of Climatic Adaptation of Tropical Cattle
Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation.
One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity
The Genetic Architecture of Climatic Adaptation of Tropical Cattle
Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation.
One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity
Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer
Genomic rearrangements are common in cancer, with demonstrated links to disease progression and treatment response.
These rearrangements can be complex, resulting in fusions of multiple chromosomal fragments and generation of derivative
chromosomes. Although methods exist for detecting individual fusions, they are generally unable to reconstruct complex
chained events. To overcome these limitations, we adopted a new optical mapping approach, allowing megabase-length genome
maps to be reconstructed and rearranged genomes to be visualized without loss of integrity. Whole-genome mapping
(Bionano Genomics) of a well-studied highly rearranged liposarcoma cell line resulted in 3338 assembled consensus genome
maps, including 72 fusion maps. These fusion maps represent 112.3 Mb of highly rearranged genomic regions, illuminating
the complex architecture of chained fusions, including content, order, orientation, and size. Spanning the junction of 147
chromosomal translocations, we found a total of 28 Mb of interspersed sequences that could not be aligned to the reference
genome. Traversing these interspersed sequences using short-read sequencing breakpoint calls, we were able to identify and
place 399 sequencing fragments within the optical mapping gaps, thus illustrating the complementary nature of optical mapping
and short-read sequencing. We demonstrate that optical mapping provides a powerful new approach for capturing a
higher level of complex genomic architecture, creating a scaffold for renewed interpretation of sequencing data of particular
relevance to human cancer.Movember Australia and the Prostate
Cancer Foundation Australia as part of the Movember Revolutionary
TeamAward to theGarvan Institute ofMedical Research. V.M.H.
is supported by the University of Sydney Foundation and Petre
Foundation, Australia.http://genome.cshlp.orgam2018School of Health Systems and Public Health (SHSPH