NGS in Forensics Genetics – examples using the GS Junior. Sponsored by Roche Diagnostics, Department of Forensic Medicine, University of Copenhagen, SUND, Martin Mikkelsen Copenhagenomics 2012
Moving Towards a Validated High Throughput Sequencing Solution for Human Iden...Thermo Fisher Scientific
Presented by Jennifer D. Churchill, PhD during a special Lunch and Learn session during the American Academy of Forensic Sciences (AAFS) 67th annual conference, February 2015. / Conclusions
• Robust panels of identity and ancestry SNPs
• Robust STR panel
• Whole genome mtDNA sequencing
• Highly informative
• Sensitive
• Quantitative – scaling comparison
• Low density chip is not necessarily a bad chip
• Wide range of density can still yield high quality data
• Based on results continue development and validation
Avances en genética. Utilidad de la NGS y la bioinformática.BBK Innova Sarea
27 Octubre 2014. Presentación de Pablo Lapunzina, Director del Instituto de Medicina Genética Médica y Molecular (INGEMM), de IDIPAZ y de CEBERER, en la "Jornada Avances en Genética y Tecnología Social. La experiencia de la Fundación Síndrome de Dravet ".
Why Y Chromosome Markers are an Ever Expanding Essential Tool in Sexual Assau...Thermo Fisher Scientific
Why Y Chromosome Markers are an Ever Expanding Essential Tool in Sexual Assault Investigations
Jack Ballantyne, Erin Hanson
National Center for Forensic Science, UCF
Sexual Assault by the numbers*:
60% of sexual assaults are not reported to the police.
97% of rapists never spend a day in jail.
There are an average of 237,868 victims of rape and sexual assault each year.
Every 2 minutes, another American is sexually assaulted.
1 out of every 5 American women have been the victim of an attempted or completed rape in her lifetime.
9 out of 10 rape victims are female.
*Source: Rape, Abuse & Incest National Network (RAINN)
In the US, an estimated 19.3% of women and 1.7% of men have been raped during their lifetimes**
**-CDC Sept 2014
NCFS Evaluation of Quantifiler® Trio / Yfiler® Plus:
Can we improve our analysis of extended interval post coital samples
using the integrated/modular Quantifiler® Trio/Yfiler® Plus system?
Conclusions:
Quantitation System
• Excellent correlation between male quantitation and profile recovery
• Negative quant (threshold based) means negative/unusable Yfiler® Plus kit
• Observed autosomal/Y results consistent with expected based upon quant and F/M ratio
Yfiler® Plus kit
• Sensitive chemistry
• If >100 pg male, most full profiles
• Results obtained with high quantities of background female DNA (up to mg)
• Many ‘Usable profiles’ F/M ranging from 333:1-100,000:1
• Y-STR profiles using YFP can be obtained at least up to 9 days after intercourse
Supporting Genomics in the Practice of Medicine by Heidi RehmKnome_Inc
View the webinar at http://www.knome.com/webinar-supporting-genomics-practice-medicine. In this presentation, Dr. Heidi Rehm, Chief Laboratory Director of the Laboratory for Molecular Medicine at Partners Healthcare and one of the Principal Investigators on ClinGen, elucidates the challenges of genomics in medicine and outlined the path to integrating large scale sequencing into clinical practice.
Moving Towards a Validated High Throughput Sequencing Solution for Human Iden...Thermo Fisher Scientific
Presented by Jennifer D. Churchill, PhD during a special Lunch and Learn session during the American Academy of Forensic Sciences (AAFS) 67th annual conference, February 2015. / Conclusions
• Robust panels of identity and ancestry SNPs
• Robust STR panel
• Whole genome mtDNA sequencing
• Highly informative
• Sensitive
• Quantitative – scaling comparison
• Low density chip is not necessarily a bad chip
• Wide range of density can still yield high quality data
• Based on results continue development and validation
Avances en genética. Utilidad de la NGS y la bioinformática.BBK Innova Sarea
27 Octubre 2014. Presentación de Pablo Lapunzina, Director del Instituto de Medicina Genética Médica y Molecular (INGEMM), de IDIPAZ y de CEBERER, en la "Jornada Avances en Genética y Tecnología Social. La experiencia de la Fundación Síndrome de Dravet ".
Why Y Chromosome Markers are an Ever Expanding Essential Tool in Sexual Assau...Thermo Fisher Scientific
Why Y Chromosome Markers are an Ever Expanding Essential Tool in Sexual Assault Investigations
Jack Ballantyne, Erin Hanson
National Center for Forensic Science, UCF
Sexual Assault by the numbers*:
60% of sexual assaults are not reported to the police.
97% of rapists never spend a day in jail.
There are an average of 237,868 victims of rape and sexual assault each year.
Every 2 minutes, another American is sexually assaulted.
1 out of every 5 American women have been the victim of an attempted or completed rape in her lifetime.
9 out of 10 rape victims are female.
*Source: Rape, Abuse & Incest National Network (RAINN)
In the US, an estimated 19.3% of women and 1.7% of men have been raped during their lifetimes**
**-CDC Sept 2014
NCFS Evaluation of Quantifiler® Trio / Yfiler® Plus:
Can we improve our analysis of extended interval post coital samples
using the integrated/modular Quantifiler® Trio/Yfiler® Plus system?
Conclusions:
Quantitation System
• Excellent correlation between male quantitation and profile recovery
• Negative quant (threshold based) means negative/unusable Yfiler® Plus kit
• Observed autosomal/Y results consistent with expected based upon quant and F/M ratio
Yfiler® Plus kit
• Sensitive chemistry
• If >100 pg male, most full profiles
• Results obtained with high quantities of background female DNA (up to mg)
• Many ‘Usable profiles’ F/M ranging from 333:1-100,000:1
• Y-STR profiles using YFP can be obtained at least up to 9 days after intercourse
Supporting Genomics in the Practice of Medicine by Heidi RehmKnome_Inc
View the webinar at http://www.knome.com/webinar-supporting-genomics-practice-medicine. In this presentation, Dr. Heidi Rehm, Chief Laboratory Director of the Laboratory for Molecular Medicine at Partners Healthcare and one of the Principal Investigators on ClinGen, elucidates the challenges of genomics in medicine and outlined the path to integrating large scale sequencing into clinical practice.
Forensic Genetics in the 21st century – meeting the challenges of biological ...Thermo Fisher Scientific
"Forensic Genetics in the 21st century – meeting the challenges of biological evidence
Presented by Peter M. Schneider, Institute of Legal Medicine
University of Cologne, Germany Human Identification Solutions Conference – Madrid, Spain
March 4, 2015 CO014206"
Next Generation Sequencing and its Applications in Medical Research - Frances...Sri Ambati
The so-called “next-generation” sequencing (NGS) technologies allows us, in a short time and in parallel, to sequence massive amounts of DNA, overcoming the limitations of the original Sanger sequencing methods used to sequence the first human genome. NGS technologies have had an enormous impact on biomedical research within a short time frame. This talk will give an overview of these applications with specific examples from Mendelian genomics and cancer research. #h2ony
Development of a Multi-Variant Frequency Ladder™ for Next Generation Sequenci...Thermo Fisher Scientific
Increasing adoption of NGS has shed light on the need for more
standardized controls to evaluate and optimize system performance.
Samples containing mutations of interest are difficult to source and cell
line pooling experiments to determine limit of detection require significant
investments of time and money. To simultaneously evaluate variant
calling performance in >200 unique amplicons across 50 genes targeted
by NGS tests, AcroMetrix® has developed a proprietary
genomic/synthetic DNA material containing over 550 mutations as a
mixture of SNV’s indels and MNP’s. The limit of detection was then
determined for >400 variants using multiple platforms. Tumor samples
were diluted with matched normal samples to mimic a range of
frequencies. Linearity between the material and diluted tumor tissue
samples were compared. Overall, highly multiplex controls with tunable
frequencies allow for much more extensive, yet streamlined, assay
evaluation and facilitate implementation and impart confidence to NGS
testing.
NGS in Clinical Research: Meet the NGS Experts Series Part 1QIAGEN
Next generation sequencing has revolutionized clinical testing but has also created novel challenges. This presentation will give an overview of state of the art clinical NGS and discuss validation, clinical implementation as well as the migration from gene panels to exome sequencing for inherited disorders with clinical and genetic heterogeneity. In addition, important shortcomings such as difficulties with regions of high sequence homology will be discussed.
NGS for Infectious Disease Diagnostics: An Opportunity for Growth Alira Health
Infectious diseases are a major public health concern causing over 3.5 million deaths worldwide. Diagnosing patients as quickly and effectively as possible is crucial for managing disease outbreaks. Next-generation sequencing (NGS) provides unique capabilities to understand the genetic profile of infectious disease patients that no other technology can match.
Whole-genome metagenomics allows clinicians to take a deeper dive into pathogens by generating big-data about their characteristics. This data can be rapidly analyzed using complex bioinformatics software algorithms to achieve clinical-grade diagnostic accuracy. In a healthcare system shifting towards personalized medicine, NGS can provide clinicians the tools that they need to prescribe individualized treatments to save patients who were previously untreatable. The result is improved quality of care, better treatment regimes, and cost-saving healthcare.
This year's 3rd Annual TCGC: The Clinical Genome Conference, held June 10-12, 2014 in San Francisco, is a three-day event that weaves together the science of sequencing and the business of implementing genomics in the clinic. It uniquely illustrates the mutual influence of those areas and the need to therefore consider the needs, challenges and opportunities of both - from next-generation sequencing and variant interpretation to insurance reimbursement and electronic health records - throughout the entire research process.Learn more at http://www.clinicalgenomeconference.com
Developing a Rapid Clinical Sequencing System to Classify Meningioma: Meet th...QIAGEN
Meningioma’s display a broad spectrum of clinical, histological and cytogenetic features even within the same WHO grade often posing a challenge for classification and prognostic stratification. In this webinar, we will describe our experience of using targeted amplicon sequencing to develop rapid clinical sequencing system to identify and confirm the meningioma genotype in just two weeks. In addition the details of the three meningioma categories and the genes involved will be discussed.
Lessons learned from high throughput CRISPR targeting in human cell linesChris Thorne
In just a short period of time CRISPR-Cas9 technology has revolutionized the field of genome editing, and taken the scientific community by storm. Already our understanding of how best to apply this technology has advanced significantly and almost every week new publications appear showcasing its application in basic and translational research.
While CRISPR-Cas9 is applicable across many different cell types, we have found it particularly suited for genome editing in near-haploid human cell lines. This has allowed us to establish a robust pipeline for the inactivation of non-essential genes at unprecedented scale and efficiency.
We have now knocked out over 1500 human genes and have generated a resource that is, to the best of our knowledge, the largest collection of human knockout cell lines available, covering comprehensive subsets of genes clustered by biological pathway (e.g. the autophagy pathway, the JAK/STAT pathway) or by phylogenetic relationship (e.g. kinases, bromodomain-containing proteins).
In this talk we will discuss how, through more than 1500 genome editing experiments, we have started to unravel some of the general principles governing the use of CRISPR-Cas9 in mammalian cells. For example, we have analyzed the impact of variation in the guide RNA sequence on Cas9 cleavage efficiency and characterized the mutational signature arising from CRISPR-Cas9 cleavage.
We will also highlight (with examples) how these learnings are now being applied to introduce other genomic modifications in a high throughput manner, including chromosomal deletions, translocations, point mutations and endogenous gene tags.
Clinical Validation of an NGS-based (CE-IVD) Kit for Targeted Detection of Ge...Thermo Fisher Scientific
In recent years, advances in next-generation sequencing (NGS) technologies have enabled faster and cheaper methods for uncovering the genetic basis of disease. For cancer, NGS based screening for known tumour subtypes can inform diagnosis and allow the clinician to tailor a specific therapy based on testing outcome. Here we present the validation of one such NGS based kit approved for CE-IVD* use to screen for specific chromosomal translocations in non-small cell lung cancer (NSCLC) samples by targeting specific breakpoints in known fusion transcripts.
The kit tested (Oncomine™ Solid Tumour Fusion Transcript Kit) included a single primer poolcontaining amplicon designs to simultaneously screen for over 75 specific rearrangements involving the receptor tyrosine kinase (RTK) genes ALK, RET and ROS1 as well as NTRK1. The panel was compatible with formalin-fixed paraffin-embedded (FFPE) lung tumour samples and achieved high sensitivity down to 10 ng of RNA input. In addition, amplicon assays designed at the 5’ and 3’ ends the RTK genes provide non-specific evidence that a translocation exists in a sample by comparing expression imbalance between the two ends. Validation testing was carried out at three external clinical laboratories (CLIA, CAP, INAB). In addition to positive and negative control samples, each site contributed FFPE lung tumour samples for which ALK fusion status was known prior to NGS library preparation carried out using the Ion AmpliSeq workflow. For site-specific samples (n=144, 16 samples per sequencing run), high concordance, sensitivity and specificity were measured at 97.2%, 90.5% and 98.4%, respectively.
Translational Genomics and Prostate Cancer: Meet the NGS Experts Series Part 2QIAGEN
Advanced prostate cancer is highly heterogeneous but this inter-patient heterogeneity has until recently not been understood. We have through an international research effort dissected the molecular landscape of advanced castration resistant prostate, elucidating key molecular targets in this group of diseases. We have also shown that PARP inhibitors have antitumor activity against a significant proportion of these cancers, mainly in men whose cancers harbor DNA repair defects.
Recent breakthroughs in genome editing technology have led to a rapid adoption that parallels that seen with RNAi. And like RNAi, these methods are taking the scientific world by storm, with high profile publications in fields as diverse as HIV treatment, stem cell therapy, food crop modification and drug development to name but a few.
Critically, the endogenous modification of genes enables the study of their function in a physiological context. It also overcomes some of the artefacts that can result from established techniques such as transgenesis and RNAi, which have mislead researchers with false positives or negatives. Until recently however genome editing required considerable technical expertise, and consequently was a relatively niche pursuit.
In this talk we will look at how the latest developments in genome editing tools have changed this, with improvements in both ease-of-use and targeting efficiency, as well as a concomitant reduction in costs opening up these approaches to the wider scientific community.
Rapid adoption of the CRISPR/Cas9 system has for example led to a long list of organisms and tissues in which genetic changes have been made with high efficiency. Other technologies such as recombinant adeno-associated virus (rAAV) offer further precision, stimulating the cell’s high-fidelity DNA repair pathways to insert exogenous sequence with unrivalled specificity. Targeting efficiency can be improved still further by using the technologies in combination – genome cutting induced by CRISPR can significantly enhance homologous recombination mediated by rAAV.
Despite these rapid advances, some pitfalls remain, and so we’ll discuss some of the key considerations for avoiding these, ranging from simply picking the right tool for the job to designing an experiment that maximises chances of success.
Finally we’ll look at how genome editing is being applied to both basic and translational research, and in both a gene-specific and genome wide manner. For the study of disease associated genes and mutations scientists can now complement wide panels of tumour cells with genetically defined isogenic cell pairs identical in all but precise modifications in their gene of interest. The ease-of-design and efficiency of the CRISPR system is also being exploited for genome wide synthetic lethality screens, facilitating rapid drug target identification with significantly reduced risk of false negatives and off-target false positives. And again, further synergies are achieved when these approaches are combined to look for potential synthetic lethal targets in specific genomic contexts.
"SNP and STR analysis using NGS
Niels Morling, MD DMSc
Professor of Forensic Genetics
Chairman & Director
Department of Forensic Medicine
Faculty of Health and Medical Sciences
University of Copenhagen
Denmark"
Forensic Genetics in the 21st century – meeting the challenges of biological ...Thermo Fisher Scientific
"Forensic Genetics in the 21st century – meeting the challenges of biological evidence
Presented by Peter M. Schneider, Institute of Legal Medicine
University of Cologne, Germany Human Identification Solutions Conference – Madrid, Spain
March 4, 2015 CO014206"
Next Generation Sequencing and its Applications in Medical Research - Frances...Sri Ambati
The so-called “next-generation” sequencing (NGS) technologies allows us, in a short time and in parallel, to sequence massive amounts of DNA, overcoming the limitations of the original Sanger sequencing methods used to sequence the first human genome. NGS technologies have had an enormous impact on biomedical research within a short time frame. This talk will give an overview of these applications with specific examples from Mendelian genomics and cancer research. #h2ony
Development of a Multi-Variant Frequency Ladder™ for Next Generation Sequenci...Thermo Fisher Scientific
Increasing adoption of NGS has shed light on the need for more
standardized controls to evaluate and optimize system performance.
Samples containing mutations of interest are difficult to source and cell
line pooling experiments to determine limit of detection require significant
investments of time and money. To simultaneously evaluate variant
calling performance in >200 unique amplicons across 50 genes targeted
by NGS tests, AcroMetrix® has developed a proprietary
genomic/synthetic DNA material containing over 550 mutations as a
mixture of SNV’s indels and MNP’s. The limit of detection was then
determined for >400 variants using multiple platforms. Tumor samples
were diluted with matched normal samples to mimic a range of
frequencies. Linearity between the material and diluted tumor tissue
samples were compared. Overall, highly multiplex controls with tunable
frequencies allow for much more extensive, yet streamlined, assay
evaluation and facilitate implementation and impart confidence to NGS
testing.
NGS in Clinical Research: Meet the NGS Experts Series Part 1QIAGEN
Next generation sequencing has revolutionized clinical testing but has also created novel challenges. This presentation will give an overview of state of the art clinical NGS and discuss validation, clinical implementation as well as the migration from gene panels to exome sequencing for inherited disorders with clinical and genetic heterogeneity. In addition, important shortcomings such as difficulties with regions of high sequence homology will be discussed.
NGS for Infectious Disease Diagnostics: An Opportunity for Growth Alira Health
Infectious diseases are a major public health concern causing over 3.5 million deaths worldwide. Diagnosing patients as quickly and effectively as possible is crucial for managing disease outbreaks. Next-generation sequencing (NGS) provides unique capabilities to understand the genetic profile of infectious disease patients that no other technology can match.
Whole-genome metagenomics allows clinicians to take a deeper dive into pathogens by generating big-data about their characteristics. This data can be rapidly analyzed using complex bioinformatics software algorithms to achieve clinical-grade diagnostic accuracy. In a healthcare system shifting towards personalized medicine, NGS can provide clinicians the tools that they need to prescribe individualized treatments to save patients who were previously untreatable. The result is improved quality of care, better treatment regimes, and cost-saving healthcare.
This year's 3rd Annual TCGC: The Clinical Genome Conference, held June 10-12, 2014 in San Francisco, is a three-day event that weaves together the science of sequencing and the business of implementing genomics in the clinic. It uniquely illustrates the mutual influence of those areas and the need to therefore consider the needs, challenges and opportunities of both - from next-generation sequencing and variant interpretation to insurance reimbursement and electronic health records - throughout the entire research process.Learn more at http://www.clinicalgenomeconference.com
Developing a Rapid Clinical Sequencing System to Classify Meningioma: Meet th...QIAGEN
Meningioma’s display a broad spectrum of clinical, histological and cytogenetic features even within the same WHO grade often posing a challenge for classification and prognostic stratification. In this webinar, we will describe our experience of using targeted amplicon sequencing to develop rapid clinical sequencing system to identify and confirm the meningioma genotype in just two weeks. In addition the details of the three meningioma categories and the genes involved will be discussed.
Lessons learned from high throughput CRISPR targeting in human cell linesChris Thorne
In just a short period of time CRISPR-Cas9 technology has revolutionized the field of genome editing, and taken the scientific community by storm. Already our understanding of how best to apply this technology has advanced significantly and almost every week new publications appear showcasing its application in basic and translational research.
While CRISPR-Cas9 is applicable across many different cell types, we have found it particularly suited for genome editing in near-haploid human cell lines. This has allowed us to establish a robust pipeline for the inactivation of non-essential genes at unprecedented scale and efficiency.
We have now knocked out over 1500 human genes and have generated a resource that is, to the best of our knowledge, the largest collection of human knockout cell lines available, covering comprehensive subsets of genes clustered by biological pathway (e.g. the autophagy pathway, the JAK/STAT pathway) or by phylogenetic relationship (e.g. kinases, bromodomain-containing proteins).
In this talk we will discuss how, through more than 1500 genome editing experiments, we have started to unravel some of the general principles governing the use of CRISPR-Cas9 in mammalian cells. For example, we have analyzed the impact of variation in the guide RNA sequence on Cas9 cleavage efficiency and characterized the mutational signature arising from CRISPR-Cas9 cleavage.
We will also highlight (with examples) how these learnings are now being applied to introduce other genomic modifications in a high throughput manner, including chromosomal deletions, translocations, point mutations and endogenous gene tags.
Clinical Validation of an NGS-based (CE-IVD) Kit for Targeted Detection of Ge...Thermo Fisher Scientific
In recent years, advances in next-generation sequencing (NGS) technologies have enabled faster and cheaper methods for uncovering the genetic basis of disease. For cancer, NGS based screening for known tumour subtypes can inform diagnosis and allow the clinician to tailor a specific therapy based on testing outcome. Here we present the validation of one such NGS based kit approved for CE-IVD* use to screen for specific chromosomal translocations in non-small cell lung cancer (NSCLC) samples by targeting specific breakpoints in known fusion transcripts.
The kit tested (Oncomine™ Solid Tumour Fusion Transcript Kit) included a single primer poolcontaining amplicon designs to simultaneously screen for over 75 specific rearrangements involving the receptor tyrosine kinase (RTK) genes ALK, RET and ROS1 as well as NTRK1. The panel was compatible with formalin-fixed paraffin-embedded (FFPE) lung tumour samples and achieved high sensitivity down to 10 ng of RNA input. In addition, amplicon assays designed at the 5’ and 3’ ends the RTK genes provide non-specific evidence that a translocation exists in a sample by comparing expression imbalance between the two ends. Validation testing was carried out at three external clinical laboratories (CLIA, CAP, INAB). In addition to positive and negative control samples, each site contributed FFPE lung tumour samples for which ALK fusion status was known prior to NGS library preparation carried out using the Ion AmpliSeq workflow. For site-specific samples (n=144, 16 samples per sequencing run), high concordance, sensitivity and specificity were measured at 97.2%, 90.5% and 98.4%, respectively.
Translational Genomics and Prostate Cancer: Meet the NGS Experts Series Part 2QIAGEN
Advanced prostate cancer is highly heterogeneous but this inter-patient heterogeneity has until recently not been understood. We have through an international research effort dissected the molecular landscape of advanced castration resistant prostate, elucidating key molecular targets in this group of diseases. We have also shown that PARP inhibitors have antitumor activity against a significant proportion of these cancers, mainly in men whose cancers harbor DNA repair defects.
Recent breakthroughs in genome editing technology have led to a rapid adoption that parallels that seen with RNAi. And like RNAi, these methods are taking the scientific world by storm, with high profile publications in fields as diverse as HIV treatment, stem cell therapy, food crop modification and drug development to name but a few.
Critically, the endogenous modification of genes enables the study of their function in a physiological context. It also overcomes some of the artefacts that can result from established techniques such as transgenesis and RNAi, which have mislead researchers with false positives or negatives. Until recently however genome editing required considerable technical expertise, and consequently was a relatively niche pursuit.
In this talk we will look at how the latest developments in genome editing tools have changed this, with improvements in both ease-of-use and targeting efficiency, as well as a concomitant reduction in costs opening up these approaches to the wider scientific community.
Rapid adoption of the CRISPR/Cas9 system has for example led to a long list of organisms and tissues in which genetic changes have been made with high efficiency. Other technologies such as recombinant adeno-associated virus (rAAV) offer further precision, stimulating the cell’s high-fidelity DNA repair pathways to insert exogenous sequence with unrivalled specificity. Targeting efficiency can be improved still further by using the technologies in combination – genome cutting induced by CRISPR can significantly enhance homologous recombination mediated by rAAV.
Despite these rapid advances, some pitfalls remain, and so we’ll discuss some of the key considerations for avoiding these, ranging from simply picking the right tool for the job to designing an experiment that maximises chances of success.
Finally we’ll look at how genome editing is being applied to both basic and translational research, and in both a gene-specific and genome wide manner. For the study of disease associated genes and mutations scientists can now complement wide panels of tumour cells with genetically defined isogenic cell pairs identical in all but precise modifications in their gene of interest. The ease-of-design and efficiency of the CRISPR system is also being exploited for genome wide synthetic lethality screens, facilitating rapid drug target identification with significantly reduced risk of false negatives and off-target false positives. And again, further synergies are achieved when these approaches are combined to look for potential synthetic lethal targets in specific genomic contexts.
"SNP and STR analysis using NGS
Niels Morling, MD DMSc
Professor of Forensic Genetics
Chairman & Director
Department of Forensic Medicine
Faculty of Health and Medical Sciences
University of Copenhagen
Denmark"
The Impact of DNA Technologies on the Future of Criminal Offender DNA DatabasesThermo Fisher Scientific
The Impact of DNA Technologies
On the Future of Criminal
Offender DNA Databases
Presented by Tim Schellberg
Gordon Thomas Honeywell Governmental Affairs
Human Identification Solutions Conference – Madrid, Spain
March 4, 2015
High-throughput processing to maximize genomic analysis through simultaneous ...Thermo Fisher Scientific
As personalized cancer care evolves, the patient’s nucleic acid becomes ever so important to provide valuable information regarding their genetic makeup and disease state. Common sample types for these analyses include biopsies, which can be very limited in material making the downstream measurement of more than one analyte rather difficult. Obtaining another biopsy, using a different section or splitting the sample can be problematic because of tumor heterogeneity. Even adjacent areas of the same tumor tissue can result in different RNA/DNA profiles so the ability to isolate multiple analytes from the same sample offer a number of benefits, which include preserving samples and data consistency eliminating any sample to sample variation. As more tests are developed to simultaneously monitor genetic alterations, there is a strong need to efficiently isolate both DNA and RNA from the same starting sample in a format compatible with high-throughput processing.
Similar to NGS in Forensics Genetics – examples using the GS Junior. Sponsored by Roche Diagnostics, Department of Forensic Medicine, University of Copenhagen, SUND, Martin Mikkelsen Copenhagenomics 2012
Similar to NGS in Forensics Genetics – examples using the GS Junior. Sponsored by Roche Diagnostics, Department of Forensic Medicine, University of Copenhagen, SUND, Martin Mikkelsen Copenhagenomics 2012 (20)
Assembling the Norway Spruce Genome: 20Gb and many challenges, Umeå Plant Sci...Copenhagenomics
Dr. Douglas G. Scofield is Principal Research Engineer at Umeå Plant Science Centre at Umeå University in Sweden. Slides for his presentation: Assembling the Norway Spruce genome.
Uncovering the impacts of circumcision on the penis microbiome, Translational...Copenhagenomics
Dr. Lance Price, Director of Center for Food Microbiology and Environmental Health
Translational Genomics Research Institute (TGen) presents his talk: Uncovering the impacts of circumcision on the penis microbiome
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
This is a presentation by Dada Robert in a Your Skill Boost masterclass organised by the Excellence Foundation for South Sudan (EFSS) on Saturday, the 25th and Sunday, the 26th of May 2024.
He discussed the concept of quality improvement, emphasizing its applicability to various aspects of life, including personal, project, and program improvements. He defined quality as doing the right thing at the right time in the right way to achieve the best possible results and discussed the concept of the "gap" between what we know and what we do, and how this gap represents the areas we need to improve. He explained the scientific approach to quality improvement, which involves systematic performance analysis, testing and learning, and implementing change ideas. He also highlighted the importance of client focus and a team approach to quality improvement.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
We all have good and bad thoughts from time to time and situation to situation. We are bombarded daily with spiraling thoughts(both negative and positive) creating all-consuming feel , making us difficult to manage with associated suffering. Good thoughts are like our Mob Signal (Positive thought) amidst noise(negative thought) in the atmosphere. Negative thoughts like noise outweigh positive thoughts. These thoughts often create unwanted confusion, trouble, stress and frustration in our mind as well as chaos in our physical world. Negative thoughts are also known as “distorted thinking”.
NGS in Forensics Genetics – examples using the GS Junior. Sponsored by Roche Diagnostics, Department of Forensic Medicine, University of Copenhagen, SUND, Martin Mikkelsen Copenhagenomics 2012
1. NGS in Forensics Genetics – Examples using the
GS Junior
Martin Mikkelsen
Section of Forensic Genetics, Department of Forensic Medicine, Faculty
of Health and Medical Sciences, University of Copenhagen
2. Current methods used in Forensic Genetics
SNPs/DIPs
X-chromosome
Y-chromosomes
mtDNA
Autosomal STR
typing
3. Agenda
Examples using the GS Junior in Forensic Genetics
STR sequencing
mtDNA sequencing
Future aspects of NGS in Forensic Genetics
GS Junior at Department of Forensic Medicine, Copenhagen
5. STR-systems
An accordion-like DNA sequence that occurs between genes
TCCCAAGCTCTTCCTCTTCCCTAGATCAATACAGACAGAAGACA
GGTGGATAGATAGATAGATAGATAGATAGATAGATAGAT
AGATAGATAGATATCATTGAAAGACAAAACAGAGATGGATGA
TAGATACATGCTTACAGATGCACAC
= 12 GATA repeats (“12” is all that is reported)
7 repeats Homozygote = both
8 repeats alleles are of the same
9 repeats length
10 repeats
Heterozygote = alleles
11 repeats
12 repeats
differ and can be resolved
from one another
13 repeats
Target region
(Short Tandem Repeat)
6. Variation in STRs
Detectable with CE Not-detectable with CE
based methods: based methods:
Variation in the number Base substitutions
of repeat units Inversions of two or
Insertion and deletion more nucleotides
of one or more Mutation in the primer
nucleotides in the binding site
amplified region
7. STR typing by sequencing using NGS
Proof-of-concept:
The long read length allows for sequencing of the whole STR
region including flanking regions
Clonal amplification allows for separation of the alleles and
haplotyping
8. Examples using the GS Junior to sequence STRs
DS21S11
Included in most STR
typing kits
A complex STR-system
3 repeat regions
[TCTA]X[TCTG]X[TCTA]3TA[TCTA]3TCA[TCTA]2TCCATA[TCTA]X
A B C
9. Case with three alleles
Child
28;30;32.2
Mother
30;32.2 28;30 30;32.2
Father
28;30;32.2 28;30
A B C
13. mtDNA in Forensic Genetics?
Cases with little or no autosomal DNA
Complicated kinship cases where the maternal inheritance
needs to be investigated
Current mtDNA investigations:
Sanger sequencing of HV1 and HV2, or control region
Typing of selected SNPs in the coding region
Advantages of full mtDNA sequencing:
15x more information than the control region
Increasing power of discrimination
MtDNA contains heteroplasmy
14. Sequencing mtDNA at Section of Forensic Genetics
• Sequencing of the whole mtDNA using the GS Junior
• 20 samples in one run
• High coverage (estimated coverage ~ 100x)
• Must be able to detect and quantify heteroplasmy
17. What does NGS give to forensic genetics?
A higher throughput!
STRs:
A system that is fully compatible with current used
technology
Database Profiles in database
CODIS (USA) 9,404,747
NDDNA (UK) 5,512,776
March 2011
Additional information from STR systems increasing the
power of discrimination
mtDNA:
Easy sequencing of the entire mtDNA
Detection and quantification of heteroplasmy
19. Future aspects of NGS in forensics
Molecular autopsy
Cardiac gene sequencing project
585 regions from 33 cardiac genes
Involved in electrical conduction in the heart
Captured using NimbleGen SeqCap EZ Library
Can be sequenced on the GS Junior with one run
Will provide additional information to pathologist performing
the autopsy
20. Future aspects of NGS in forensics
Patient suffering from Brugada syndrome
Carrying a mutation in the SCN5A gene (R121W)
21. Future aspects of NGS in forensics
Forensic
Toxicology
Forensic
NGS Genetics
Forensic
Pathology
The ultimate forensic
autopsy report
22. Acknowledgements
Section of Forensic Genetics:
Marlene Andersen
Stine Hansen
And…
Eszter Rockenbauer
Anders J. Hansen
Rune Frank-Hansen
Claus Børsting
Michael Stangegaard
Niels Morling
Anja Jørgensen
Nadia Jochumsen
Maibritt Sigvardt