Authored by Ahmed A Bashir,
Dr. Bashir and his group at Al Mana Group frequently take care
of and try to provide a genetic diagnosis for children with seriously
disabling neurodevelopment and neuromuscular disorders. Even
with comprehensive genetic testing, a clear molecular basis can
remain elusive.Since many of these children are likely to have an
undetected cause of their disorder, we propose here to develop
an international collaboration between Dr. Bashir and Dr. Nelson
to collect appropriate biomaterials for identification of causal
mutations and push the envelope of detection of causal mutations
by integrating RNAsequencing with whole genome sequencing and
developing inexpensive models for improving the utility of RNAsequencing
for neurodevelopmental disorders.Developmental
disorders are frequently due to genetic mutations and can be
detected in about 30% of cases using whole exome sequencing.
Thus, the first screen for the included subjects is exomesequencing
of an index case in the family. If a successful identification of a
mutation is identified, these results are returned to the Al Mana
Group to request ordering of a specifically developed molecular
test through the UCLAOrphan Disease Testing Center on all relevant
family members.
This effectively serves as a powerful and thorough
screen to identify those individuals who have a readily identifiable
genetic disease.The remaining 70% of the cohort to be collected,
will be subjected to short read based whole genome sequencing at
UCLA. These data are able to sensitively detect, genome-wide, all
SNVs and small indels (an average of 5 million per genome). We are
thus well powered to observe DE NOVO mutations. However, there
are over 60 de novo mutations per genome and only one is even
potentially causal for a given rare autosomal dominant disease.
Thus, interpretation of the functional consequence on RNA reading
frame is imperative. Here we propose to use RNAsequencing of
non-neural tissues to delineate ORF defects and intersect with
the WGS DNA sequencing. We intend that this will result in higher
rate of patient diagnosis at a molecular level and lead to insights
of disease pathogenesis.For this project, we request consent and
samples from Patients of Al ManaGroup which may include blood,
skin, and saliva to study both RNA and DNA. We request fibroblast
from skin punch in order to grow cells that can be de differentiated
into iPSCs and then into a neural phenotype to induce expression of
mRNAs expressed in brain or muscle. This is not a treatment study
but may lead to insights towards new therapies.
Genome-wide diagnostic toolshaverapidly become an
indispensable aspect of care for individuals with rare genetic
disorders, frequently providing information on inheritance and
prognosis, and in some cases direct therapeutic insights. The
success of wholeexome sequencing (WES) in our clinical practice
over the last 5 years strongly supports the proposition that largescale
genetic information will be a major component of Precision
Health throughout the lifespan[1]. However, even with the genetic
definition of over 5,000 rare diseases, which in aggregate affect
millions of Americans, a specific molecular diagnosis is returned
after WES to only 30% of individuals tested[1-4]. While this is
a major advance, 70% remain undiagnosed even with strong
evidence of a genetic disorder. This is likely due to many factors,
including incomplete genome coverage, poor detection of certain
classes of structural variation (SV), especially within repeats,
andthe vast identification of single nucleotide variants and SVs
whose significance is uncertain.
Here, we propose to improve the detection of disease causing
rare recessive and de novo autosomal dominant variants and
improve the utility of whole genome sequencing (WGS)for genetic
diagnosis of rare diseases.We propose to improve WGS coverage to
better assess repeat regions, deletion/duplications, and SV using
long-read DNA sequencing. Further, we propose to determine
functional consequence through integrated transcriptome analysis
of both high depth short-read and long-read RNA sequencing. Investigation of a DNA alteration that affects splicing or RNA
abundance has long been recognized to be important (A,B,C) and
has been demonstrated to substantially improve the interpretation
of VUS[5]. However, clinical cDNA sequencing is not used broadly
for diagnostics, andRNA-sequin this context has been largely
limited to research, so theestablishment of clinical WGS/RNAseqtools
developed here, developsamore complete genomics and
bioinformatics infrastructure for comprehensive genomic analysis
that is critical to future precision patient management more
broadly.By conducting this project in well-selected patients with
undiagnosed, and likely genetic, diseases, in whom WES has been
negative, we leverage the tremendous ongoing clinical effort for
rare disease diagnosis based on WES. All of the tools developed here
are designed to be readily extended to all undiagnosed diseases,
establishing a feasible framework for adoption by other clinical
laboratories.
Here, we pilot an integrated approach toinclude
transcript tome data in the more routine interpretation of WGS of
individuals with neurodevelopmental disorders(ND) by analyzing
the transcriptome from patient derived blood and skin fibroblasts.
To increase the likelihood of observing expression, these libraries
are normalized, which allows us to observe about 85% of all
neurological disease genes from one of these two non-neurological
tissue sources. While these tissue types are not ideal, for ND the
affected tissue (i.e. brain) is not readily possible to biopsy, thus
alternate cell types are beneficial for understanding DNA mutation
effects on mRNA, as they represent a broad sampling of gene
expression and can be readily and ethically accessed in genetics
clinics throughout our network, including at the County facilities.
This lessens burden of participation and broadens accessibility,
which are key aspects to implementation in relation to precision
medicine. We hypothesize that implementing RNA-seqwhen jointly
analyzed with more complete WGS that includes sensitive search
for structural variants (SV)will substantially increase diagnostic
rate. Identifying the genetic cause of an individual’s disease has
immediate impact on their clinical care, providing clarity on
inheritance within the family and guidance for treatment. The
final WGS/RNA-seq clinical test will be complex but will in this
proposal be implemented as a series of transferable protocols.
The data analysis pipelines proposed here require substantial
optimization on custom compute server configurations that include
field programmable gated arrays(FPGA) through a collaboration
with Falcon Computing, a commercial partner. This hardware
acceleration has already reduced the server footprint by a factor
of 10 and accelerated the task of WGS analysis of a human genome
by 10-fold.
This demonstration project is intended todevelop and
implement a novel and complex WGS/RNA-seq diagnostic for those
individuals for whom even exomesequencing fails to identify the
causal mutation.Here, we select for comprehensivegenomic analysis
a core group of 50 patients and relevant family members seen in
clinical practice by Dr. Bashir and colleagues in the Al Mana Group
(total ~150 subjects)with pediatric neurologic or neuromuscular
disorders. All individuals will be consented for genomic sequencing
and provision of appropriate biomaterials.All 50 affected individuals
will be sequenced by whole exomeseuqencing to screen for known
disease-causing mutations.Most of these 50 individuals, from our
experience of sequncing over 4,000 individuals at UCLA will be
negative for a causal mutation. We estimate that 33 families will then
be tested in the below molecular assays (approx. 100 individuals).
This will provide the opportunity for new gene discovery and
create the framework for ongoing collaboration between UCLA
and Al Mana Group.In all cases, neither parent is affected, and
the inheritance pattern is consistent with either a rare recessive
model or a de novoautosomal dominant model. Strategically, ten
of the selected individuals have an exome-identifiedVUS that has
some evidence that the variantimpactsthe Open Reading Frame
(ORF), and these along with variants in canonical splice acceptor/
donor sites will serve as positive controls of the RNA analysis to
resolve mRNA effect of the DNA variant. Samples will be selected
from the clinical judgment of Al Mana Group physicians, so that
the breadth and utility of the approach is demonstrated across the
group of relevant patients in Saudi Arabia.
This workflow greatly
benefits from the tremendous ongoing clinical efforts at our UC
Health campuses to identify the genetic cause of rare diseases.We
will observe the relative value of each WGS/RNA-seq technology
in identifying mutations that disrupt ORFs of mRNA by comparing
groups of patient TRIOs. Here, we will assay33TRIOs withaugmented
short read 30x oversampling of the human genome using Illumina
technology with comprehensive long read DNA sequencing to more
sensitively observe SVs and deletions/duplications and determine
their pathologic consequence. These data will be integrated with
deep whole transcriptome RNA sequencing from tissue libraries
using short read technologies.A subset of unsolved cases will have
long read mRNA analysis to attempt resolve RNA consequence.
The integration of these assays should greatly improve structural
variation detection over the broadest possible size range and
directly observe its consequence on mRNA abundance or ORF to
augment interpretation.
Here we push the envelope of SV detection to augment the high
sensitivity and accuracy of SNV and small INDEL detection from
Illumina short read technology. To improve haplotyping, which
simplifies and improves base calling, libraries for sequencing
at HLI will be prepared using 10X GenomicsChromium Genome
Library kit[6]. The major improvement will be in the arena of SV,
which is not sensitively resolved by short reads: deletions and
duplications in the range of a few hundred base pairs to kilobases
are difficult to reliably detect genome-wide. Potential common
sources of mutation that are invisible include tandem repeat array
variations, inversions, deletions or duplications that are flanked by
repeat sequences, and ALU and LINE insertions. Long repeats of
high sequence similarity confound the ability to fully read a human
diploid genome with short reads. Long single molecule reads
greatly facilitate diploid human genome assembly when combined
with short reads[7-9], providing unprecedented power to observe
important mutation types such as (Figure1).
LINE insertions[10] or complex structural variation.The
approach here is to have a set of complementary technologies to
resolve a wide range of disease-causing mutations, ranging from
single base variants through large SV. All 50 trios will be subjected
to very long read single molecule BioNano GenomicsIrys assay in
order to identify larger scale structural variation and to resolve
complex, repeat laden genomic regions.Irys uses a two different
restriction sequences to nick and tag the genome with a fluorescent
marker at positions of known sequence, then through nano
channels[11] measure the distance between marker which in effect
makes a physical or optical map of the human genome[12-16],
permitting detection of deletions as small as 1kb. Since the mean
read length is 350kb, this technology allows spanning of complex
and highly repetitive sequence in the human genome, and sizing of
large tandem repeats. We have applied the Irys system to accurately
detect large or complex deletions and partial gene duplications in
DMDin both affected maleDMD patients and carrier mothers. Based
on these experiences and technical capability, we will generate
mean 75x genome coverage. There is about 5% failure to label
at any given potential nicking site, and base level resolution is
not obtained. However, at 75x mean coverage there is negligible
contribution to miscalling of deletions/duplications in the range of
10kb to 300kb. Of known deletions in a pilot set of genomes, in the
range of 5-50kb, we have 95% sensitivity of detection using two
enzymes.Determining specificity and appropriate determination of
support from short reads is an aim of the analytical plan.All SV will
be mapped to predict consequence on mRNA abundance/ORF of
all known ND genes genome-wide. Support for these mRNA effect
predictions will be sought through RNA-seqand matched to the
known disease model.
The thorough DNA sequence generated in aim 1 will provide
high-resolution SNVand SV information, but it will remain critical
to determine consequence of variants on the ORF of mRNA through
transcriptome analysis as many detected DNA variants will not be
possible to interpret. As demonstrated recently, the addition ofRNAseq
can greatly facilitate the determination of pathogenicity of
seemingly benign variation detected by WES or WGS. For instance,
missense or synonymous DNA variants detected by WEScan create
strong splice acceptors or donors and result in aberrant splicing[5].
Similarly, deep intronic variants not within the canonical splice
acceptor or donor sequences can create strong pseudo exons that
are included in the mature mRNA and disrupt reading frame[5]. To
increase sensitivity and to gain understanding of the potential to
increase diagnostic yield from WGS, we will augment DNA sequence
with RNA analysis[17,18].For neurodevelopmental disorders, the
affected tissue type isoften not available (i.e. brain). Thus, use of
more available tissue types, blood and dermal fibroblasts, still
provides substantial information and allows the approach to be
practically implemented within most genetics clinics, as blood draw
and skin punch are routinely performed in clinics.
It is obvious that
since these cell types are not necessarily affected by the mutations
causing brain disorders or other syndromic disorders, the affected
gene may not be well expressed in these tissues and this does
diminish the utility of RNA analysis. However, we note that without
normalization, 50% of all neurodevelopmental disease genes
are observed at greater than 2 FPKM in one of these cell types
(internal reference data). To improve the depth of coverage of low
expression genes, we will employ cDNA normalization strategy.
Whole blood will be collected in PAXgene tubes and placed on ice
for transport so that high quality long RNA can be purified safely
within 24 hours. Skin punches will be placed in culture to generate
mRNA from fibroblasts in 2-3 weeks. These two tissue types are
nicely complementary in expression pattern[5]. To increase the
proportion of the neurodevelopmentally-relevant transcriptome
that are sufficiently covered to observe allele specific expression,
we will subject the long fragment cDNA library to duplex specific
nuclease (DSN) based normalization (Evrogen)[19-24]. All of
the individuals in Group A that are not clearly resolved and fully
interpretable from Aim 1, will be subjected to this normalized RNA analysis. Initial RNA Analysis will consist of 200 million
fragments paired end 100bp reads on the Illumina platform, which
allows observation of exon junctions from split read and read-pair
mapping. Apparently causal defects will be confirmed by RT-PCR.
A)We will implement a state of the art pipeline for WGS analysis
using the customized computing technology developed by Falcon
Computing to accelerate analysis by an order of magnitude with
field programmable gate arrays (FPGAs). This technology was
originally developed by the Center for Domain Specific Computing
(CDSC) at UCLAdirected by Prof. J. Congwith the support of NSF
and Intel under the Expeditions in Computing and Innovation
Transition (InTrans) Programs. A single Falcon computing
appliance, with a physical footprint of 2Userver, can perform whole
genome alignment and variant calling through GATK best practice
pipeline in an average of 5 hours (100+ hours in our high RAM
compute nodes). This acceleration removes a key obstacle to the
use of WGS interpretation in the clinical setting and substantially
lowers barriers towards adoption. Under the direction of Prof. Cong
with Prof. E. Eskin, these appliances will be tuned to accelerate
alignments and integration of the 75x BioNano genomics data
Reducing compute times is an important to implement in clinical
practice allowing greater flexibility to meet reasonable turnaround
time and creating a more robust computational pipeline.
We will integrate the more complete WGS with RNA-seq,
withtranscript abundance, splicing, phasing of variants in
mRNA[25],and allele specific expression data to both guide
interpretation of WGS and provide evidence for variant
pathogenicity. We willassess the improvement in diagnostic
rate and specificity of RNA-seq coupled with WGS, as compared
with WES alone (E). We will specifically determine the rate of
pathogenic or likely pathogenic mutation/variant identification for
the 33individuals with completer WGS more coupled with RNA-seq
relative to WES data, and compare with the inferences possible from
WGS RNA-seqof whole blood from short read technology alone.We
will further enumerate the number of loss-of-function DNA variants,
based on the combined analysis withRNA and better SV resolution
across all parental samples that are consistent with detection of a
carrier state for any rare recessive disease as an additional measure
of pathogenic variant detection assessment.
Primarily, the genomic
and transcriptomic data generated will be assessed for their utility
in diagnosing children with rare ND disorders, but we will also
broadly consent families for datasharingsuch that these data can
be used as a reference. Since fibroblasts will be available as well
additional genome-wide or targeted datasets can be gathered
in the future to assess relevance to the identification of rare and
common variation.We will also use these data to bench mark
improvements in DNA sequence assembly algorithms.Thus, this
pilot project serves not only to extend the sensitivity of genomic
assessment in rare diseases,but will be a flagship project of central
importance to the development of precision medicine on the UCLA
campus and in partnership with the Al Mana Group to explore
improvements in genetic diagnosis and utility of comprehensive
genetic assessments made possible by genome technology.Because
of this importance to our efforts at UCLA, we are able to leverage
personnel and computational resources through the launch of the
UCLA Precision Health Institute.These complementary activities
enable a more robust diagnostic developmental pipeline.
Our
project builds specific collaborations with BioNano Genomics
and Falcon Computing, HLI, and uses two California technologies
(Illumina and Pacific Biosciences) and partners with all 5 UC
campuses and some of the LA County facilities.By completing these
aims we will have made major inroads in developing translational
infrastructure for precision medicine for undiagnosed patients, and
integrating RNA-seq and WGS into clinical practice, important steps
towards developing best practices for Precision Health in California
and in Saudi Arabia.We note that while the above pilot process is
expensive, ongoing improvements in technology development, and
perhaps a tiered diagnostic approachwill permit more thorough
genome assessment at reasonable costs. For the participants of
this research study, each predicted causal DNA mutation identified
from this pilot will not be directly reported to the physician/
family, but rather after discussion in the GDB with the ordering
physician,specific testing is ordered through the UCLA Orphan
Disease Testing Center.All relevant and interested individuals
within the family can be tested with the developed family-specific
DNA diagnostic. A clinical report is generated through the UCLA
Molecular Pathology Diagnostic Lab with Dr. Wayne Grody.
This project will develop and assess a more
comprehensivediagnostic process intended toimprove the
full interpretation of individual human diploid genomes and
reveal mRNA consequence of non-coding DNA variants with
implementation into clinical practice. Our ability to improve our
competency in clinical genome interpretation is an essential
aspect of precision medicine. This collaboration will informtwoway
communication channels between laboratory and clinicians.
The developed enterprise will enhance novel gene discoveryfor
ultra-rare diseases, which can lead to strong genetically tailored
therapeutic insights.Finally, this pilot will allow us to develop
efficient algorithms for the joint analysis of RNA and DNA and
implement them on more optimized hardware solutions, which are
transferable to other centers.
In the last 3 years, we and our colleagues have performed
CESon over 1600 patients. Per the NIH, ~7% of patients asking for
their help have an undiagnosed disease. The cost of these clinical
investigations, in the absence of clear diagnostic protocols, is high.
For example, the estimated lifetime medical care cost for a person
with intellectual disability, often associated with undiagnosed
disorders, was around $1M in 2003 (F) and contributes to the
economic strains on medical systems. Improving diagnostic yield provides
closure for families affected by rare diseases, improves the
clarity of prognostic information, and allows for meaningful genetic
counseling regarding family planning[26,27].
An integrated WGS/RNA-seq diagnosticrequires several
separate analytical inputs, tracking, and computational integration.
Critical bottlenecks that slow the proposed diagnostic test will be
systematically addressed. We will be continuously altering software
and hardware components to harmonize timing of component
analyses.Interpretation of the final data will be a challenge, even
with interpretation through the GDB. Even long read technologies
such as Iso-Seq do not read through long transcripts such as DMD
(~14Kb) or TTN (~110Kb), and allele specific expression of low
expression genes may not be adequately observed from whole
blood or fibroblasts. Thus, gaps will remain. Development of
individual induced neural cells using iPSCs and more sequencing
of diverse populations canreduce these gaps. The participants
arehighly motivated families who have already undergone CES, but
our physicians may experience difficulty enrolling due to patient
movement within the health system or interest in data sharing.
Since there is a growing group of exome-negative individuals, we are
confident of recruitment goals.Establishing a full CAP/CLIA system
is the goal at the end of the project, and it will be challenging to codevelop
standard operating procedures and implement within the
Molecular Diagnostics Laboratories as all aspects of the technical
system, analytical system and interpretation system need to be
fully validated to permit clinical reporting of variants. We may need
to rely on ODTC reporting of identified variants. We faced similar
challenges during the initial 6 month implementation of CES,among
the first in the US. Given the clinical, bioinformatic, hardware, and
genomic expertise assembled for this project, we anticipate similar
progress.
Dr. S. Nelsonhas 25 years of genomics experience and
established CES for rare disease diagnosis on the UCLA campus will
serve as overall PI on the site campus with additional key leadership
from Dr. A. Bashir of the Al Mana Group. Dr. Bashir will effectively
serve the role as physician and consenter of the relevant patients in
Saudi Arabia, and as postdoctoral fellow at UCLA in the Nelson Lab
which will allow ?Dr. Bashir to participate in all aspects of the assay
development, interpretation, and drafting of manuscripts from the
collaborative work.Much of the work will occur under the auspices
of the Department of Human Genetics at UCLA and the Institute for
Precision Health at UCLA.
None.
No Conflict of Interest.
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