EMMA, a cost- and time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in 1,525 patients

AbstractThe mechanisms driving clonal heterogeneity and evolution in relapsed pediatric acute lymphoblastic leukemia (ALL) are not fully understood. We performed whole genome sequencing of samples collected at diagnosis, relapse(s) and remission from 29 Nordic patients. Somatic point mutations and large-scale structural variants were called using individually matched remission samples as controls, and allelic expression of the mutations was assessed in ALL cells using RNA-sequencing. We observed an increased burden of somatic mutations at relapse, compared to diagnosis, and at second relapse compared to first relapse. In addition to 29 known ALL driver genes, of which nine genes carried recurrent protein-coding mutations in our sample set, we identified putative non-protein coding mutations in regulatory regions of seven additional genes that have not previously been described in ALL. Cluster analysis of hundreds of somatic mutations per sample revealed three distinct evolutionary trajectories during ALL progression from diagnosis to relapse. The evolutionary trajectories provide insight into the mutational mechanisms leading relapse in ALL and could offer biomarkers for improved risk prediction in individual patients.

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Development of All-Plastic Microvalve Array for Multiplexed Immunoassay

Volume 10: Micro- and Nano-Systems Engineering and Packaging ◽

10.1115/imece2014-38154 ◽

2014 ◽

Author(s):

Shancy Augustine ◽

Pan Gu ◽

Xiangjun Zheng ◽

Toshikazu Nishida ◽

Z. Hugh Fan

Keyword(s):

Large Scale ◽

Low Cost ◽

Simultaneous Detection ◽

Cost Effective ◽

Negative Control ◽

Sensitive Material ◽

Detection Scheme ◽

Power Battery ◽

Multiple Analytes ◽

Multiplexed Immunoassay

There is a need for low-cost immunoassays that measure the presence and concentration of multiple harmful agents in one device. Currently, comparable immunoassays employ a one-analyte-per-test format that is time consuming and not cost effective for the requirement of detecting multiple analytes in a single sample. For instance, if a spectrum of harmful agents, including E. coli O157, cholera toxin, and Salmonella typhimurium, should be simultaneously monitored in foods and drinking water, then a one-analyte-per-test would be inefficient. This work demonstrates a platform capable of simultaneous detection of multiple analytes in a single, low-cost, microvalve array-enabled multiplexed immunoassay. This multiplexed immunoassay platform is demonstrated in a prototype COC (cyclic olefin copolymer) device with a 2×3 array in which 6 analytes can be detected simultaneously. In order to contain and regulate the flow of reagents in the multichannel device, an array of microfluidic valves actuated by a thermally expandable material and microfabricated resistors have been developed to direct the flow to the necessary assay sites. The microvalve-based immunoassay is shown to be reliable, easy to operate, and compatible with large-scale integration. The all-plastic microvalves use paraffin wax as the thermally sensitive material which drastically reduces power consumption by latching upon closing so that pulsed power is required only to close and latch the microvalve until it is necessary to re-open the valve. The multiplexed detection scheme has been demonstrated by using three proteins, C reactive protein (CRP) and transferrin, both of which are biomarkers associated with traumatic brain injury (TBI) as well as bovine serum albumin (BSA) as the negative control. Since there are no external bulky pneumatic accessories required to operate/latch the microvalves in the device, this compact, thermally actuated and latching microvalve-enabled multiplexed immunoassay has the potential to realize a portable, low power, battery operated microfluidic device for biological assays.

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Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples

Oncotarget ◽

10.18632/oncotarget.11259 ◽

2016 ◽

Vol 7 (38) ◽

pp. 61845-61859 ◽

Cited By ~ 13

Author(s):

Márton Zsolt Enyedi ◽

Gábor Jaksa ◽

Lajos Pintér ◽

Farkas Sükösd ◽

Zoltán Gyuris ◽

...

Keyword(s):

Simultaneous Detection ◽

Genomic Rearrangements ◽

Brca Mutations ◽

Large Genomic Rearrangements ◽

Ffpe Tumor

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Mitochondrially targeted ZFN s for selective degradation of pathogenic mitochondrial genomes bearing large‐scale deletions or point mutations

EMBO Molecular Medicine ◽

10.1002/emmm.201303672 ◽

2014 ◽

Vol 6 (4) ◽

pp. 458-466 ◽

Cited By ~ 139

Author(s):

Payam A Gammage ◽

Joanna Rorbach ◽

Anna I Vincent ◽

Edward J Rebar ◽

Michal Minczuk

Keyword(s):

Large Scale ◽

Point Mutations ◽

Mitochondrial Genomes ◽

Selective Degradation

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SVFX: a machine-learning framework to quantify the pathogenicity of structural variants

10.1101/739474 ◽

2019 ◽

Cited By ~ 2

Author(s):

Sushant Kumar ◽

Arif Harmanci ◽

Jagath Vytheeswaran ◽

Mark B. Gerstein

Keyword(s):

Machine Learning ◽

Large Scale ◽

Three Dimensional ◽

Point Mutations ◽

Dimensional Structure ◽

Rapid Decline ◽

Ras Signaling ◽

Cancer Genes ◽

Structural Variations ◽

Pathogenic Variants

AbstractA rapid decline in sequencing cost has made large-scale genome sequencing studies feasible. One of the fundamental goals of these studies is to catalog all pathogenic variants. Numerous methods and tools have been developed to interpret point mutations and small insertions and deletions. However, there is a lack of approaches for identifying pathogenic genomic structural variations (SVs). That said, SVs are known to play a crucial role in many diseases by altering the sequence and three-dimensional structure of the genome. Previous studies have suggested a complex interplay of genomic and epigenomic features in the emergence and distribution of SVs. However, the exact mechanism of pathogenesis for SVs in different diseases is not straightforward to decipher. Thus, we built an agnostic machine-learning-based workflow, called SVFX, to assign a “pathogenicity score” to somatic and germline SVs in various diseases. In particular, we generated somatic and germline training models, which included genomic, epigenomic, and conservation-based features for SV call sets in diseased and healthy individuals. We then applied SVFX to SVs in six different cancer cohorts and a cardiovascular disease (CVD) cohort. Overall, SVFX achieved high accuracy in identifying pathogenic SVs. Moreover, we found that predicted pathogenic SVs in cancer cohorts were enriched among known cancer genes and many cancer-related pathways (including Wnt signaling, Ras signaling, DNA repair, and ubiquitin-mediated proteolysis). Finally, we note that SVFX is flexible and can be easily extended to identify pathogenic SVs in additional disease cohorts.

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Genomic rearrangements of the CDKN2A locus are infrequent in Italian malignant melanoma families without evidence of CDKN2A/CDK4 point mutations

Melanoma Research ◽

10.1097/cmr.0b013e328319412f ◽

2008 ◽

Vol 18 (6) ◽

pp. 431-437 ◽

Cited By ~ 7

Author(s):

Marina Vignoli ◽

Maria Chiara Scaini ◽

Paola Ghiorzo ◽

Roberta Sestini ◽

William Bruno ◽

...

Keyword(s):

Malignant Melanoma ◽

Point Mutations ◽

Genomic Rearrangements ◽

Cdkn2a Locus

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Ataxias with Autosomal, X-Chromosomal or Maternal Inheritance

Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques ◽

10.1017/s0317167100007733 ◽

2009 ◽

Vol 36 (4) ◽

pp. 409-428 ◽

Cited By ~ 25

Author(s):

Josef Finsterer

Keyword(s):

Ataxia Telangiectasia ◽

Large Scale ◽

Autosomal Recessive ◽

Autosomal Dominant ◽

Late Onset ◽

Fragile X ◽

Axonal Neuropathy ◽

Friedreich Ataxia ◽

Point Mutations ◽

Spinocerebellar Ataxias

Heredoataxias are a group of genetic disorders with a cerebellar syndrome as the leading clinical manifestation. The current classification distinguishes heredoataxias according to the trait of inheritance into autosomal dominant, autosomal recessive, X-linked, and maternally inherited heredoataxias. The autosomal dominant heredoataxias are separated into spinocerebellar ataxias (SCA1-8, 10-15, 17-23, 25-30, and dentato-rubro-pallido-luysian atrophy), episodic ataxias (EA1-7), and autosomal dominant mitochondrial heredoataxias (Leigh syndrome, MIRAS, ADOAD, and AD-CPEO). The autosomal recessive ataxias are separated into Friedreich ataxia, ataxia due to vitamin E deficiency, ataxia due to Abeta-lipoproteinemia, Refsum disease, late-onset Tay-Sachs disease, cerebrotendineous xanthomatosis, spinocerebellar ataxia with axonal neuropathy, ataxia telangiectasia, ataxia telangiectasia-like disorder, ataxia with oculomotor apraxia 1 and 2, spastic ataxia of Charlevoix-Saguenay, Cayman ataxia, Marinesco-Sjögren syndrome, and autosomal recessive mitochondrial ataxias (AR-CPEO, SANDO, SCAE, AHS, IOSCA, MEMSA, LBSL CoQ-deficiency, PDC-deficiency). Only two of the heredoataxias, fragile X/tremor/ataxia syndrome, and XLSA/A are transmitted via an X-linked trait. Maternally inherited heredoataxias are due to point mutations in genes encoding for tRNAs, rRNAs, respiratory chain subunits or single large scale deletions/duplications of the mitochondrial DNA and include MELAS, MERRF, KSS, PS, MILS, NARP, and non-syndromic mitochondrial disorders. Treatment of heredoataxias is symptomatic and supportive and may have a beneficial effect in single patients.**Please see page 424 for abbreviation list.

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