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臨床ゲノムシーケンシングおよび診断における進歩:概要

Advances in Clinical Genome Sequencing and Diagnostics

発行 Insight Pharma Reports 商品コード 264963
出版日 ページ情報 英文
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臨床ゲノムシーケンシングおよび診断における進歩:概要 Advances in Clinical Genome Sequencing and Diagnostics
出版日: 2013年03月25日 ページ情報: 英文
概要

当レポートでは、臨床ゲノムシーケンシングにおける近年の人気の高まりについて、シーケンシングプロバイダー、これらのサービスを提供する医療組織、およびさまざまな解読サービス・プラットフォーム・ビジネスモデルを提供する新興企業の観点から分析しており、臨床ゲノムシーケンシングの前進、臨床データの作成とその解読をリードする組織、遺伝病で確認された変異体の原因の決定、がんにおける臨床ゲノムシーケンシング、アカデミック・民営の臨床ゲノムプロバイダー、次世代シーケンシング情勢、ゲノム解読ソフトウェアの提供企業、シーケンシング標準設定のイニシアチブ、専門家へのインタビュー、および臨床ゲノムシーケンシングの顧客調査結果などをまとめ、概略下記の構成で取り上げております。

イントロダクション

第1章 臨床ゲノムシーケンシングの進歩

  • 概念実証
  • 既知から未知へ
  • 診断探求の終わり
  • 調査戦略
  • 原因変異体とデータベース
  • がんゲノミクス
  • 結論

第2章 臨床ゲノミクスのパイオニア・プロバイダー

  • アカデミックメディカルセンター
  • 商業部門

第3章 臨床レベルのシーケンシング

  • 次世代シーケンシングの情勢
  • ゲノム解読ソフトウェア
  • ゲノム標準

第4章 INSIGHT PHARMA REPORTSによる臨床ゲノミクス調査

  • 調査の質問:どのタイプのラボで働いていますか?
  • 施設はCLIA認証を受けていますか?
  • 施設はCAP認証を受けていますか?
  • 施設の場所はどこですか?
  • どのシーケンシング器具を使用していますか、またそれぞれどのくらい所有していますか?
  • シーケンシングプロバイダーにアウトソースしたことはありますか?
  • どのシーケンシングプロバイダーを利用したことがありますか?
  • ラボで実施する1次シーケンシング作業は何ですか?
  • 今後12ヶ月間で新しいシーケンシング装置の購入を検討していますか?
  • どのシーケンシングプラットフォームをどれだけ購入しようと考えていますか?
  • 最もよく利用する商業マッピング/アセンブリー/バリアントコーラー(Caller)プラットフォームのタイプは何ですか?
  • 主に利用するその他のNGS(次世代シーケンシング)ソフトウェア/プラットフォームは何ですか
  • 医療レベルのゲノムを提供するコストはどれくらいになると推計しますか?
  • ゲノムシーケンシング全体を臨床へ統合するにあたっての最大の課題は何だと思いますか?
  • クラウドでのNGSデータの保存または分析の経験がありますか?
  • 臨床データをクラウドに置きますか?

第5章 ソートリーダーへのインタビュー

参考資料

付録

追加情報/リソース

企業インデックス

図表

目次

Abstract

Author: Kevin Davies, PhD

This report explores the recent surge in clinical genome sequencing, from the point of view of the sequencing providers, the medical organizations delivering these services, and the start-ups offering a variety of interpretation services, platforms, and business models. Aspects discussed and presented include:

  • Progress in clinical genome sequencing
  • Organizations leading the way in generating clinical data and its interpretation.
  • Determining the causality of documented variants in genetic disease.
  • Clinical genome sequencing in oncology.
  • Academic and commercial clinical genomics providers.
  • The next-gen sequencing landscape.
  • Companies providing genome interpretation software.
  • Initiatives in setting sequencing standards.
  • Interviews with six industry experts, conducted exclusively for this report.
  • Results of a custom survey on clinical genome sequencing.
  • A list of print and online resources for further investigation into this area.

For many years now, next-generation sequencing (NGS) has been used in clinical research, building on the success of being able to sequence personal genomes affordably, and turning that technology into defining the mutation profile of rare Mendelian diseases and cancer. With the first report of successful exome sequencing in a patient with a mystery illness, the clinical community has embraced NGS-performed in CLIA- and CAP-certified laboratories-for diagnostic testing.

Nevertheless, at the $1,000-5,000 price point, medical practitioners face a dilemma: It is possible to offer to sequence the exome or complete genome of a patient for roughly the same price as a traditional patented genetic diagnostic test or gene panel. Economics alone would appear to dictate that the practice of medical genetics and clinical diagnostics must evolve radically in the face of the remarkable advances in NGS. That sentiment has been bolstered in recent years with more and more anecdotal stories of the identification of mutations in patients suffering mysterious/undiagnosed (presumably) genetic disorders. Emboldened by these success stories, medical centers, sequencing platform providers, and diagnostics companies are rethinking their strategies for delivering exome and/or whole-genome sequencing services.

In a further irony, the cost of sequencing has fallen so fast that it is now a relatively trivial component of the full array of services required to deliver clinical genome information-what some have (literally or tongue-in-cheek) called the $100,000 or $1 million interpretation. Leaving aside the apples-and-oranges debate of the precise cost of genome interpretation, there is no doubt that 2012 proved to be a stunning year for the maturation of clinical genome testing. Several prominent, public stories relating to the successful end of diagnostic odysseys provide gratifying examples of the potential of this technology. Cases of families receiving a confirmed diagnosis after years of false hope and hundreds of thousands of dollars in medical costs show the benefit of this approach, and beg the question of how long the molecular diagnostics industry will continue in its single-gene/multigene panel approach. (After all, the exome is essentially just one giant gene panel with 22,000 genes.)

Exciting, remarkable progress in clinical genome sequencing is being fueled by steady advances in existing platforms, the arrival of new diagnostic platforms, and improvements in genome analysis software. That said, the adoption of clinical NGS is not trivial, and many questions still remain about setting standards, ensuring analytic and clinical validity of the tests, and reimbursement.

About the Author

Kevin Davies, PhD, is the founding editor of Bio-IT World and the journal Nature Genetics. He is the author of three books that explore the impact of technology and genomics in medicine, most recently "The $1,000 Genome" (Free Press, 2010). Kevin also serves as an advisor to Cambridge Healthtech Associates and blogs at NGS Leaders.

Table of Contents

Introduction

Chapter 1 - PROGRESS IN CLINICAL GENOME SEQUENCING

  • 1.1. Proof of Concept
  • 1.2. From Known to Unknown
  • 1.3. Ending Diagnostic Odysseys
  • 1.4. Search Strategy
  • 1.5. Causal Variants and Databases
  • 1.6. Cancer Genomics
  • 1.7. Conclusions

Chapter 2 - CLINICAL GENOMICS PIONEERS AND PROVIDERS

  • 2.1. Academic Medical Centers
    • Medical College of Wisconsin
    • Baylor Whole Genome Laboratory
    • UCLA Medical Genetics Clinic
    • Children's Hospital of Philadelphia (CHOP)
    • Emory Genetics Laboratory
    • Genomics and Pathology Services, Washington University in St. Louis (GPS@WUSTL)
    • Fox Chase Cancer Center, Philadelphia
  • 2.2. Commercial Sector
    • Ambry Genetics
    • GeneDx
    • EdgeBio
    • Foundation Medicine
    • Courtagen Life Sciences
    • GeneInsight-Illumina Network

Chapter 3 - CLINICAL-GRADE SEQUENCING

  • 3.1. The Next-Gen Sequencing Landscape
    • Illumina HiSeq/MiSeq
    • Ion Torrent
    • Complete Genomics
    • Pacific Biosciences (PacBio)
    • Qiagen/IBS
    • Nanopore Sequencing: Oxford Nanopore, Genia Technologies, and More
    • Oxford Nanopore
    • Genia Technologies
    • Other Technologies
  • 3.2. Genome Interpretation Software
    • Ingenuity Systems
    • Omicia
    • SV Bio
    • Cypher Genomics
    • Personalis
    • Knome
    • InVitae Corporation
    • Genomatix
    • Station X
  • 3.3. Genome Standards
    • The CLARITY Challenge
    • Sequencing Standards
    • Genome in a Bottle
    • The Archon Genomics X PRIZE

Chapter 4 - INSIGHT PHARMA REPORTS' CLINICAL GENOMICS SURVEY

  • Survey Questions:What Type of Lab Do You Work In?
  • Is Your Facility CLIA-Certified?
  • Is Your Facility CAP-Certified?
  • Where Is Your Facility Located?
  • Which Sequencing Instruments Do You Use and How Many of Each Do You Have?
  • Have You Outsourced To Any Sequencing Provider?
  • Which Sequencing Providers Have You Used?
  • What Is the Primary Sequencing Work Done In Your Lab?
  • Are You Considering Purchasing Any New Sequencing Equipment In the Next 12 Months?
  • Which Sequencing Platforms Are You Considering Purchasing and How Many?
  • What Type of Commercial Mapping/Assembly/Variant Caller Platform Do You Mostly Use?
  • What Other NGS Software/Platforms Do You Principally Use?
  • What Software Do You Use for Medical Genome Interpretation?
  • What Would You Estimate the Cost of Delivering a Medical-Grade Genome to Be?
  • What Do You Consider the Biggest Challenge In Integrating Whole-Genome Sequencing Into The Clinic?
  • Do You Have Any Experience Storing or Analyzing NGS Data In the Cloud?
  • Would You Put Clinical Data In the Cloud?

Chapter 5 - THOUGHT LEADER INTERVIEWS

  • 5.1. Nazneen Aziz, PhD
    • Director of Molecular Medicine, Transformation Program Office, College of American Pathologists (CAP)
  • 5.2. Elizabeth Worthey, PhD
    • Assistant Professor, Medical College of Wisconsin
  • 5.3. Ashley Van Zeeland, PhD
    • CEO, Cypher Genomics, San Diego, CA
  • 5.4. Ron Ranauro
    • Founder/Managing Partner, Incite Advisors
  • 5.5. Karen Seibert, PhD
    • Professor, Department of Genetics, Washington University in St. Louis
    • Director, Genetics and Pathology Services (GPS@WUSTL), Washington University School of Medicine
  • 5.6. Catherine Brownstein, MPH, PhD
    • Project Manager, The Gene Partnership's Research Sequencing Division, Boston Children's Hospital

References

Appendix

FURTHER INFORMATION/RESOURCES

Company Index

FIGURES

  • Figure 1.1. Filtration Decision Tree for Genomic Variants
  • Figure 2.1. GeneDx Letter for Pre-Authorization (Edited)
  • Figure 3.1. The Rapidly Falling Cost of Genome Sequencing

SURVEY FIGURES:

  • Figure 4.1. What Type of Lab Do You Work In?
  • Figure 4.2. Is Your Facility CLIA-Certified?
  • Figure 4.3. Is Your Facility CAP-Certified?
  • Figure 4.4. Where Is Your Facility Located?
  • Figure 4.5. Which Sequencing Instruments Do You Use and How Many of Each Do You Have?
  • Figure 4.6. Have You Outsourced To Any Sequencing Provider?
  • Figure 4.7. Which Sequencing Providers Have You Used?
  • Figure 4.8. What Is the Primary Sequencing Work Done In Your Lab?
  • Figure 4.9. Are You Considering Purchasing Any New Sequencing Equipment In the Next 12 Months?
  • Figure 4.10. Which Sequencing Platforms Are You Considering Purchasing and How Many?
  • Figure 4.11. What Type of Commercial Mapping/Assembly/Variant Caller Platform Do You Mostly Use?
  • Figure 4.12. What Other NGS Software/Platforms Do You Principally Use?
  • Figure 4.13. What Software Do You Use for Medical Genome Interpretation?
  • Figure 4.14. What Would You Estimate the Cost of Delivering a Medical-Grade Genome to Be?
  • Figure 4.15. What Do You Consider the Biggest Challenge In Integrating Whole-Genome Sequencing Into The Clinic?
  • Figure 4.16. Do You Have Any Experience Storing or Analyzing NGS Data In the Cloud?
  • Figure 4.17. Would You Put Clinical Data In the Cloud?

TABLES

  • Table 1.1. Proof-of-Concept Identification of Mutation in Freeman-Sheldon Syndrome Exomes
  • Table 1.2. Companies Applying NGS Toward Cancer Diagnostics and Treatment
  • Table 3.1. Projected Sequence Throughput for Ion Proton Chips
  • Table 3.2. Potential Advantages of Nanopore Sequencing
  • Table 3.3. Comparison of HugeSeq to Other Genome Analysis Platforms
  • Table 3.4. Categorization of Clinical Variants by InVitae
  • Table 3.5. The CLARITY Challenge Contestants and Finalists
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