Biomedical Informatics Year in Review

1
Biomedical Informatics Year in Review

• Daniel R. Masys, MD
• Professor and Chair
• Department of Biomedical Informatics
• Professor of Medicine
• Vanderbilt University School of Medicine

2
2007 Year in ReviewContent for this session is
athttp//dbmichair.mc.vanderbilt.edu/amia2007/
including citation lists and linksand this
PowerPoint
3
Design for this Session

• Modeled on American College of Physician Update
  sessions
• Emphasis on what it is and why it is
  important
• 1-2 examples of each in detail and others in
  synopsis
• Audience interaction for each category of item
  discussed

4
Source of Content for Session

• Literature review of RCTs indexed by MeSH term
  Medical Informatics, Telemedicine
  descendents or main MeSH term Bioinformatics,
  and publication date between November 2006 and
  October 2007 (n42), further qualified by
  involvement of gt100 providers or patients
• Poll of American College of Medical Informatics
  fellows list

5
Thanks to
It takes a village

• Betsy Humphreys
• George Hripcsak
• Bonnie Kaplan
• Denis Protti
• Don Simborg
• David States
• Paul Tang
• Mark Tuttle
• William Yasnoff

• Rebecca Jerome
• Andrew Balas
• Marion Ball
• Dominic Covvey
• Robert Dolin
• Sherrilynne Fuller
• Terri Hannan
• Brian Haynes
• Bill Hersh

6
Topics

• Representative New Literature
• Notable Events the Top Ten list

7
New Literature Highlights Clinical Informatics

• Unintended consequences of clinical information
  technology
• Clinical Decision Support
• Telemedicine
• The practice of informatics

8
New Literature Highlights Bioinformatics and
Computational Biology

• Human Health and Disease
• The practice of bioinformatics

9
Unintended consequences of clinical information
technology
10
(No Transcript)
11
Unintended Consequences of Information
Technologies

• Reference
• Linder et al., Arch Intern Med. 2007 Jul
  9167(13)1400-5. Brigham Womens Hospital
• Title
• Electronic health record use and the quality of
  ambulatory care in the United States.
• Aim
• Assess effects of Electronic Health Records on
  quality of care delivered in ambulatory settings
• Methods
• Retrospective, cross-sectional analysis of 17
  quality measures from 2003-2004 National
  Ambulatory Medical Care Survey, correlated with
  use of EHRs.

12
Unintended Consequences of Information
Technologies

• Reference
• Linder et al., Arch Intern Med. 2007 Jul
  9167(13)1400-5.
• Results
• EHRs used in 18 of 1.8 billion visits
• For 14 of 17 quality measures, fraction of visits
  where recommended best practice occurred was no
  different in EHR settings than manual records
  settings.
• 2 better with EHR avoiding benzodiazepines in
  depression, avoiding routine urinalysis
• 1 worse with EHR prescribing statins for
  hypercholesteremia (33 vs. 47, p0.01)
• Conclusion
• As implemented, EHRs not associated with better
  quality ambulatory care

13
Unintended Consequences of Information
Technologies

• Reference
• Linder et al., Arch Intern Med. 2007 Jul
  9167(13)1400-5.
• Importance
• Received disproportionate media attention due to
  reactionary message
• Lost in the media hype Less than 40 of EHR
  implementations have all elements important for
  effects on quality (e-prescribing, test ordering,
  results, clinical notes, decision support).
• Best performance regardless of infrastructure was
  suboptimal (lt 50 adherence to best practice).

14
Clinical Decision Support for Providers

• Reference
• Raebel MA et al. J Am Geriatr Soc. 2007
  Jul55(7)977-85. Kaiser Permanente, Denver,
  Colorado
• Title
• Randomized trial to improve prescribing safety in
  ambulatory elderly patients.
• Aim
• To determine whether a computerized tool that
  alerted pharmacists when patients aged 65 and
  older were newly prescribed potentially
  inappropriate medications was effective in
  decreasing the proportion of patients dispensed
  these medications.
• Methods
• 60,000 pts randomized evenly in intervention
  group pharmacists got e-alerts for 11 types of
  medication

15
Clinical Decision Support for Providers

• Reference
• Raebel MA et al J Am Geriatr Soc. 2007
  Jul55(7)977-85.
• Results
• Over 1 year, 543 (1.8) of intervention groups
  over age 65 were prescribed targeted meds, vs.
  644 (2.2) of usual care group (P 0.002)
• Statistically significant drop in use of
  amitryptiline and diazepam.
• Importance
• Adds to extensive literature on reducing Adverse
  Drug Effects via alerts and reminders
• Targeting healthcare team members who can modify
  physician orders has beneficial effect
• Note Similar design study of meds during
  pregnancy reported in JAMIA July-Aug 2007

16
Clinical Decision Support for Providers

• Reference
• Bailey T et al. Arch Intern Med. 2007 Mar
  26167(6)586-90. Wash U., St. Louis
• Title
• An intervention to improve secondary prevention
  of coronary heart disease.
• Aim
• Determine whether alerts sent to pharmacists,
  combined with academic detailing by
  pharamacists, change physician prescribing
  behavior.
• Methods
• RCT randomizing patients with acute MI in
  hospital setting to alerts sent to pharmacist
  based on elevated troponin I levels. Pharmacists
  receiving alerts reviewed inpt meds list and
  communicated with care providers.

17
Clinical Decision Support for Providers

• Reference
• Bailey T et al. Arch Intern Med. 2007 Mar
  26167(6)586-90.
• Methods, contd
• Outcome measures proportion of Pts discharged on
  ASA, beta-blockers, ACE inhibitors, and statins.
• Results
• Improved compliance with ACE and statin
  guidelines, no impact on beta blockers or ASA.
• When all 4 classes of drugs considered together,
  84 (305 of 365 eligible) intervention vs. 70
  (343 of 488) in control received recommended
  therapy (Plt0.001)
• Importance
• Routing messages to pharmacists, combined with
  academic detailing, provides useful model for
  systematic improvements in care

18
Clinical Decision Support

• Reference
• Chaudhry R et al. Arch Intern Med. 2007 Mar
  26167(6)606-11. Mayo Clinic
• Title
• Web-based proactive system to improve breast
  cancer screening a randomized controlled trial.
• Aim
• Improve mammography screening rates using alerts
  and reminders directed at appointment
  secretaries.
• Methods
• Web-based preventive care reminder system created
  to alert staff making appointments about
  screening mammography.
• 6600 patients signed up for study, randomized to
  usual care or use of system that sent a letter or
  e-mail message in advance of screening data, and
  provided response status to appt. secretary.

19
Clinical Decision Support

• Reference
• Chaudhry R et al. Arch Intern Med. 2007 Mar
  26167(6)606-11.
• Results
• Screening rate for annual mammography was 64 in
  intervention group vs. 55 in control group
  (Plt.001)
• No difference in intervention vs. control on any
  other preventive service.
• Conclusion
• Practice re-design to send reminder messages to
  appointment secretary rather than to physician
  provider improved compliance with preventive care
  services guidelines.
• Importance
• More evidence that care team members other than
  physicians are better targets for information
  interventions designed to increase consistency of
  care.

20
Clinical Decision Support for Providers

• 3 RCTs on Tobacco Cessation
• Unrod et al. Randomized controlled trial of a
  computer-based, tailored intervention to increase
  smoking cessation counseling by primary care
  physicians. J Gen Intern Med. 2007
  Apr22(4)478-84. Mt. Sinai, NYC
• Wadland WC et al Practice-based referrals to a
  tobacco cessation quit line assessing the impact
  of comparative feedback vs general reminders. Ann
  Fam Med. 2007 Mar-Apr5(2)135-42. Michigan
  State
• Bentz CJ et al. Provider feedback to improve 5A's
  tobacco cessation in primary care a cluster
  randomized clinical trial. Nicotine Tob Res. 2007
  Mar9(3)341-9. Providence/St. Vincent,
  Portland, OR

21
Clinical Decision Support for Providers

• Methods
• Mt. Sinai study Computer tailored one page
  summary to physician and patient re Smoking
  Cessation Guidelines (5As Assess, Advise,
  Assist-written, Assist-referral, Arrange).
  Measured adherence to 5As guidelines, and
  smoking cessation success at 6 months
• MSU study Provider specific feedback on smoking
  cessation referrals vs. general reminders.
  Measured referral numbers and quit rate at 18
  months.
• Providence Portland study Provider specific
  monthly feedback reports vs. no feedback from
  state tobacco quitline.

22
Clinical Decision Support for Providers

• Results
• All three studies showed statistically improved
  compliance with 5As guidelines by providers and
  increased in referrals for cessation help (Odds
  ratios 2.7 5)
• All showed increased numbers of patients quitting
  smoking at borderline statistical significance
  levels vs. control groups
• Conclusion
• Modest positive impacts of proactive (tailored
  information sheet) and retrospective (regular
  feedback reports on numbers of referrals) smoking
  cessation interventions
• Interventions judged to be cost effective and are
  continuing
• Importance
• Approximately the same results in a CDSS area
  (smoking cessation) from three different sites
  with similar intervention and process/outcomes
  measures
• Information intervention necessary but not
  sufficient to achieve optimal outcomes

23
Clinical Decision Support for Providers

• Reference
• Rothschild JM, et. al. Transfusion. 2007
  Feb47(2)228-39. Brigham and Womens, Boston
• Title
• Assessment of education and computerized decision
  support interventions for improving transfusion
  practice.
• Aim
• Reduce overuse of blood products via a CDSS
  intervention.
• Methods
• Random assignment of junior house officers to
  receiving education and CPOE-based decision
  support at time of ordering blood products.
• Orders classified as DS-agree or DS-disagree
• DS-disagree charts reviewed for appropriateness

24
Clinical Decision Support for Providers

• Reference
• Rothschild JM, et. al. Transfusion. 2007
  Feb47(2)228-39.
• Results
• Inappropriate non-emergent transfusion at
  baseline was 72 in both interventional and
  control groups.
• Improved to 63 with conventional education.
• DS intervention group continued to improve to
  59.
• Physicians accepted 14 of DS-recommended orders,
  especially recommendations to increase dose
  (73).
• Conclusion
• Education and CDSS had statistically significant
  reduction of inappropriate transfusion orders,
  though residual amount remained high.
• Impact
• Dont be sanguine about expecting CDSS to change
  prescribing

25
Clinical Decision Support for Providers

• Reference
• Kheterpal et al. Anesth Analg. 2007
  Mar104(3)592-7. Univ. Michigan
• Title
• Electronic reminders improve procedure
  documentation compliance and professional fee
  reimbursement.
• Aim
• To evaluate alert system to improve documentation
  of care for increased reimbursement.
• Methods
• Automated system scanned EMR for surgical
  procedures using arterial catheters, sent e-mail
  and/or pager reminder to provider if no procedure
  note about catheter placement.
• Residents and CRN anesthetists randomized to msg
  or no msg

26
Clinical Decision Support for Providers

• Reference
• Kheterpal et al. Anesth Analg. 2007
  Mar104(3)592-7.
• Results
• Baseline compliance rate 80
• During 2 month study, 88 of intervention group
  completed documentation requirements vs. 75 of
  control.
• After RCT ended, all staff got reminder and
  compliance rose to 98
• Professional fee reimbursement projected to
  increase 40,500 over 12 months.
• Conclusion
• Documentation deficiencies amenable to
  alerts/reminders
• Impact
• ADSS works in a fashion similar to CDSS, perhaps
  better

27
Clinical Decision Support for Patients

• Reference
• Thompson RG et al. Qual Saf Health Care. 2007
  Jun16(3)216-23. Univ Newcastle, UK
• Title
• A patient decision aid to support shared
  decision-making on anti-thrombotic treatment of
  patients with atrial fibrillation randomised
  controlled trial.
• Aim
• To determine the efficacy of a computerised
  decision aid in patients with atrial fibrillation
  making decisions on whether to take warfarin or
  aspirin therapy.
• Methods
• 109 Pts with a. fib randomized to computerized
  DSS vs. pamphlet on ASA vs. warfarin
• Outcomes decision conflict scale, and therapy
  choice

28
Clinical Decision Support for Patients

• Reference
• Thompson RG et al. Qual Saf Health Care. 2007
  Jun16(3)216-23.
• Results
• Decision conflict lower in CDSS group (ie.,
  happier with decision made)
• CDSS Pts agreed to start coumadin only 25 of
  time when recommended by physician, vs. 94 of
  printed guidelines group
• Conclusion
• CDSS for patients can empower them to feel
  comfortable about decisions that are medically
  suboptimal
• Impact
• Increased understanding mediated by CDSS systems
  is a double edged sword

29
Clinical Decision Support for Patients

• Reference
• Saitz R et al. Alcohol Alcohol. 2007
  Jan-Feb42(1)28-36. Boston Univ.
• Title
• Screening and brief intervention online for
  college students the ihealth study.
• Aim
• To test the feasibility of online alcohol
  screening and brief intervention (BI) by
  comparing (i) two approaches to inviting all
  students to be screened, and (ii) a minimal
  versus a more extensive BI.
• Methods
• All freshman students(4008) sent one of two
  e-mail invitations to participate in alcohol
  counseling online application either invitation
  for general health assessment, or invitation for
  alcohol assessment

30
Clinical Decision Support for Patients

• Reference
• Saitz R et al. Alcohol Alcohol. 2007
  Jan-Feb42(1)28-36
• Methods, contd
• Participants with unhealthy alcohol use randomly
  assigned to minimal or more extensive information
  intervention
• Follow-up after one month for those receiving
  interventions
• Results
• 55 of students completed online screening, no
  difference if invitation specifically mentioned
  alcohol vs. general health.
• 37 of male students and 26 of female students
  had unhealthy alcohol use.
• More extensive intervention caused more students
  to expression interest in changing behavior
• 75 of intervention completed second assessment,
  and of these unhealthy behaviors reduced by 33
  in women and 15 in men.

31
Clinical Decision Support for Patients

• Reference
• Saitz R et al. Alcohol Alcohol. 2007
  Jan-Feb42(1)28-36
• Conclusion
• Over half of freshman class reached by e-mail and
  completed health risk assessment
• Mention of alcohol not a deterrent to
  participation
• Brief online intervention appeared to have
  favorable short term impact.
• Impact
• Contibutes to literature on self-reporting of
  health conditions traditionally considered
  stigmatizing

32
Clinical Decision Support for Patients

• 2 RCTs on Smoking Cessation
• Strecher VJ et al. Moderators and mediators of a
  web-based computer-tailored smoking cessation
  program among nicotine patch users. Nicotine Tob
  Res. 2006 Dec8 Suppl 1S95-101. Univ. Michigan
• Japuntich et al. Smoking cessation via the
  internet a randomized clinical trial of an
  internet intervention as adjuvant treatment in a
  smoking cessation intervention. Nicotine Tob Res.
  2006 Dec8 Suppl 1S59-67. Univ Wisconsin
  Madison

33
Clinical Decision Support for Patients

• Methods
• Michigan study 3971 smokers who purchased
  nicotine patches randomized to standard web-based
  materials vs. tailored web intervention.Measured
  abstinence at 12 weeks.
• Wisconsin study 284 smokers randomized to
  bupropion counseling /- access to an online
  support group and information site. Measured
  abstinence at 12 weeks and 24 weeks.

34
Clinical Decision Support for Patients

• Results
• Michigan study found tailored program more
  effective by number abstinent in certain
  subgroups (children at home, frequent alcohol
  use, tobacco-related illness present) but not
  significant for groups as whole
• Wisconsin study found use of online resources
  correlated with smoking abstinence, but no
  overall difference in abstinence between groups.
• Conclusion
• Targeted information interventions help a subset
  of smokers to quit who would not otherwise
• Importance
• Addiction interventions are a difficult area of
  therapeutics, for which informatics has a modest
  role to play

35
New CDSS RCTs showing no difference for
intervention vs. control

1. Curtis et al. Challenges in improving the quality
   of osteoporosis care for long-term glucocorticoid
   users a prospective randomized trial. Arch
   Intern Med. 2007 Mar 26167(6)591-6.
2. Glassman et al. The utility of adding
   retrospective medication profiling to
   computerized provider order entry in an
   ambulatory care population. J Am Med Inform
   Assoc. 2007 Jul-Aug14(4)424-31.
3. Schapira et al. Decision-making at menopause a
   randomized controlled trial of a computer-based
   hormone therapy decision-aid. Patient Educ Couns.
   2007 Jul67(1-2)100-7.
4. Tuil et al. Empowering patients undergoing in
   vitro fertilization by providing Internet access
   to medical data. Fertil Steril. 2007
   Aug88(2)361-8.

36
Clinical Decision Support

• Questions and Comments

37
Telemedicine

• 12 new RCTs published
• November 2006 October 2007

• 3 chronic airways disease
• 2 psychiatric care
• 2 diabetes care
• 2 imaging dermatology and ophthalmology
• 1 each prostate cancer, cardiac rehab,
  hypertension

38
Telemedicine

• 3 RCTs on airways disease
• Chan DS et al. Internet-based home monitoring
  and education of children with asthma is
  comparable to ideal office-based care results of
  a 1-year asthma in-home monitoring trial.
  Pediatrics. 2007 Mar119(3)569-78. Tripler Army
  Medical Center, Honolulu
• Jan RL et al. An internet-based interactive
  telemonitoring system for improving childhood
  asthma outcomes in Taiwan. Telemed J E Health.
  2007 Jun13(3)257-68. National Cheng Kung
  University, Taiwan
• Whitten P, Mickus M. Home telecare for COPD/CHF
  patients outcomes and perceptions. J Telemed
  Telecare. 2007 13(2)69-73. Michigan State
  University

39
Telemedicine

• Methods
• Tripler study 120 asthma pts age 6-17 randomized
  to same clinical pathway with follow-up either
  via office visit or website interaction. Measured
  medication adherence, PFTs
• Taiwan study 88 asthma pts randomized to either
  Internet care guidance and spirometry reporting,
  or printed materials and spirometry diary.
  Measured self-reported symptoms, spirometry
  results, quality of life, knowledge of disease
• Michigan State study 161 pts with COPD/CHF
  randomized to home care visits in person or via
  telemedicine unit. Measured SF-36, patient
  perceptions, physiologic status at beginning and
  end of study.

40
Telemedicine

• Results
• Taiwanese study found telemedicine group had
  better adherence to meds, better PFTs.
• Other two studies found clinical equivalence of
  telemedicine and face-to-face visits at home or
  office
• Impact
• Adds to substantial literature showing
  therapeutic equivalency of telemedicine vs. in
  person monitoring of chronic airways disease.

41
Telepsychiatry

• 2 RCTs
• Fortney JC et al. A randomized trial of
  telemedicine-based collaborative care for
  depression. J Gen Intern Med. 2007
  Aug22(8)1086-93. Epub 2007 May 10. VA Health
  Svcs Research, Little Rock AR
• O'Reilly R. Is telepsychiatry equivalent to
  face-to-face psychiatry? Results from a
  randomized controlled equivalence trial.
  Psychiatr Serv. 2007 Jun58(6)836-43. Regional
  Mental Healthcare, London, Ontario, Canada

42
Telepsychiatry

• Methods
• VA study 395 pts with moderately severe
  depression followed at small VA community clinics
  without psychiatrists. Measured med adherence,
  treatment response, quality of life, pt
  satisfaction with treatment.
• Canadian study 495 pts referred for initial
  psych consultation randomized to telepsych
  interview or face-to-face consult. Measured
  health status, patient satisfaction, costs

43
Telepsychiatry

• Results
• VA study supplementing usual care with
  telemedicine psych consultation improved
  medication adherence and therapeutic response.
  Also found higher patient satisfaction, and
  better quality of life measures in intervention
  group.
• Canadian study found equivalence for
  telepsychiatry outcomes and face to face
  outcomes, with 10 decrease in overall costs for
  telemedicine based care.
• Impact
• Telemedicine technologies can extend subspecialty
  support to primary care settings
• Telepsychiatry equivalent to F2F as perceived by
  Pts

44
Tele-imaging

• 2 RCTs
• Conlin PR et al. Nonmydriatic teleretinal
  imaging improves adherence to annual eye
  examinations in patients with diabetes. J Rehabil
  Res Dev. 2006 Sep-Oct43(6)733-40. Boston VA
• Pak H, et al. Store-and-forward teledermatology
  results in similar clinical outcomes to
  conventional clinic-based care. J Telemed
  Telecare. 200713(1)26-30. Army TATRC, Fort
  Dietrick MD

45
Tele-imaging

• Methods
• VA study 448 pts randomized to annual dilated
  eye exam vs. non-dilated screening image with
  remote interpretation, followed by in person
  consult if indicated. Measured correspondence of
  remote and in person findings, and adherence to
  annual exam schedule
• Army study 776 pts randomized to face-to-face
  dermatology consult vs. telemedicine via store
  and forward imaging text description

46
Tele-imaging

• Results
• VA study Strong but not perfect correlation of
  tele-imaging with dilated in person exam.
  Improvement in compliance with annual screening.
  Patient acceptance high.
• Army study found equivalence of diagnosis and
  ongoing monitoring of response to therapy for
  teledermatology and in person care.
• Impact
• Store and forward telemedicine lends itself well
  to specialties where static images are keys to
  diagnosis and follow-up

47
2006-7 Telemedicine RCTs

• Continue 30 year history of showing equivalence
  of telemedicine for selected types of home
  monitoring, chronic disease follow-up, and visual
  diagnosis
• Only 1 of 12 addressed cost vs. benefit
• Leave unaddressed principal historical
  impediments to telemedicine acceptance
  reimbursement, licensure, liability

48
Telemedicine

• Questions and Comments

49
Practice of Informatics

• Reference
• Beebe TJ et al. Health Serv Res. 2007 Jun42(3
  Pt 1)1219-34. Mayo Clinic
• Title
• Mixing web and mail methods in a survey of
  physicians.
• Aim
• To assess the effects of two different mixed-mode
  (mail and web survey) combinations on response
  rates, response times, and nonresponse bias in a
  sample of primary care and specialty internal
  medicine physicians.
• Methods
• Randomized 500 physicians at Mayo clinic to
  receiving either a mailed paper survey on EMR, or
  web link for online survey, with cross over.

50
Practice of Informatics

• Reference
• Beebe TJ et al. Health Serv Res. 2007 Jun42(3
  Pt 1)1219-34.
• Results
• Overall response rate higher with mailed survey
  sent first than web link sent first (70 vs.
  63).
• Results obtained 2 days faster with web survey
• Key outcome variables no different in paper vs.
  web survey methods
• Impact
• Some insight on approaches to surveying
  physicians in large institutional setting

51
Practice of Informatics

• Reference
• Tideman R et al. Sex Transm Infect. 2007
  Feb83(1)52-6. Univ. of Melbourne, Australia
• Title
• A randomised controlled trial comparing
  computer-assisted with face-to-face sexual
  history taking in a clinical setting.
• Aim
• To compare computer-assisted self-interview
  (CASI) with routine face-to-face interview (FTFI)
  for sexual history taking from patients in a
  clinical setting.
• Methods
• Randomized 713 new walk-in patients at STD clinic
  to CASI or FTFI initial assessment. CASI
  subsequently had FTFI.

52
Practice of Informatics

• Reference
• Tideman R et al. Sex Transm Infect. 2007 Feb
  83(1)52-6.
• Methods, contd
• Comparison of self-reported risk behaviors,
  concordance of CASI and FTFI assessments.
• Results
• 85 of CASI pts comfortable with method
• Results equivalent except that women using CASI
  reported more male partners than in FTFI setting,
  and CASI users reported Hep B vaccination more
  often.
• Conclusion
• CASI efficient and acceptable method for
  gathering sexual risk data in STD clinic setting

53
Practice of Informatics

• Reference
• Bates B, et al. J Cancer Educ. 2007
  Spring22(1)15-20. Ohio Univ.
• Title
• The effect of improved readability scores on
  consumers' perceptions of the quality of health
  information on the internet.
• Methods
• 519 community participants randomized to receive
  lung cancer prevention level at 8th grade reading
  level, 9th grade, or first year college reading
  level.
• Measured perceived trustworthiness, readability,
  completeness.

54
Practice of Informatics

• Reference
• Bates B, et al. J Cancer Educ. 2007
  Spring22(1)15-20.
• Results
• Reducing reading level had no significant effect
  on perceived readability, trustworthiness, or
  completeness.
• Conclusion
• Conventional wisdom about relationship of
  readability and effectiveness not supported in
  this study
• Importance
• Of potential relevance to IRBs and guidelines for
  informed consent documentation

55
Practice of Informatics

• Reference
• Schneider S. et al. Oncol Nurs Forum. 2007
  Jan34(1)39-46. Duke Univ.
• Title
• Virtual reality a distraction intervention for
  chemotherapy.
• Aim
• To explore virtual reality (VR) as a distraction
  intervention to relieve symptom distress in
  adults receiving chemotherapy treatments for
  breast, colon, and lung cancer.
• Methods
• 123 patients in cross-over design, serving as own
  control. Received Virtual Reality headset as
  distraction during chemotherapy at one visit, and
  not the next.

56
Practice of Informatics

• Reference
• Schneider S. et al. Oncol Nurs Forum. 2007
  Jan34(1)39-46..
• Methods, contd
• Measured symptom distress, fatigue, anxiety, open
  ended questionnaire regarding experience.
• Results
• Using VR made chemotherapy treatment seem shorter
  and pts liked VR treatment sessions better than
  std.
• However, no difference in symptom distress
  immediately or at 2 days post treatment

57
Practice of Informatics

• Reference
• Schneider S. et al. Oncol Nurs Forum. 2007
  Jan34(1)39-46..
• Conclusions
• VR distraction can make chemotherapy treatments
  more palatable but do not decrease
  therapy-associated symptoms
• Impact
• Pharmacology trumps perceptual psychology in
  chemotherapy settings

58
Practice of Informatics

• Questions and Comments

59
New Literature Highlights Bioinformatics and
Computational Biology

• Human Health and Disease
• The practice of bioinformatics

60
Bioinformatics Human Health Disease

• Reference
• The Wellcome Trust Case Control Consortium.
  Nature 447, 661-678 (7 June 2007)
• Title
• Genome-wide association study of 14,000 cases of
  seven common diseases and 3,000 shared controls.
• Aim
• To find genetic determinants of 7 major diseases
  using single nucleotide polymorphism (SNP)
  assessments at 500,000 loci, in 14,000 patients
• Methods
• 54 centers in UK enrolled 14,000 volunteers,
  whose DNA was genotyped with Affymetrix 500K SNP
  chip.
• Case control study design

61
Bioinformatics Human Health Disease

• Reference
• The Wellcome Trust Case Control Consortium.
  Nature 447, 661-678 (7 June 2007)
• Results
• 24 association signals significant at P lt 10e-7
• 1 in bipolar disorder, 1 in coronary disease, 9
  in Crohns disease, 3 in Rheumatoid arthritis, 7
  in type I diabetes, 3 in type 2 diabetes
• 58 other SNP polymorphisms with differences at
  10e-5 to 10e-7
• Importance
• The era of genome-wide scans has arrived.
• Personalized medicine based on individual SNPs
  and linked SNP patterns (ie., haplotypes) will
  significantly inform personalized disease
  prevention, diagnosis and treatment
• Level of complexity will make decision support
  rules and CDSS essential

62
Bioinformatics Human Health Disease

• Reference
• Estivill et al. PLoS Genet. 2007 Oct
  193(10)1787-99.
• Title
• Copy number variants and common disorders
  filling the gaps and exploring complexity in
  genome-wide association studies.
• Aim
• Discussion of contribution of gene Copy Number
  Variation (CNV) to human disorders.
• Methods
• Literature review of GWAS studies and
  contribution of CNV to explaining genetic
  diversity

63
Bioinformatics Human Health Disease

• Reference
• Estivill et al. PLoS Genet. 2007 Oct
  193(10)1787-99.
• Results
• Reduplicated genes account for some of the
  unexplained variation seen in genome-association
  studies.
• CNVs not detected by standard SNP technologies,
  but have been shown to contribute to genetic
  variance in Parkinsons disease, Alzheimer,
  Autism, retardation, and chronic pancreatitis
• Importance
• Copy Number Variation is an important new genetic
  concept that will have relevance in explaining
  complex traits and some diseases

64
Bioinformatics Human Health Disease

• Reference
• Levy et al. PLoS Biol 5(10) e254
• Title
• The Diploid Genome Sequence of an Individual
  Human.
• Aim
• Full genome sequence of J. Craig Venter, compared
  to consensus published human genome sequence
• Methods
• Standard DNA sequencing technologies applied to
  single individual rather than small group of
  reference samples

65
Bioinformatics Human Health Disease

• Reference
• Levy et al. PLoS Biol 5(10) e254
• Results
• Comparing Venters DNA to NCBI reference human
  sequence shows 4.1 million variants 3.2M SNPs,
  53K block substitutions, 292K heterozygous
  insert/delete events (indels), 559K homozygous
  indels
• Non-SNP variability accounts for 74 of variant
  bases.
• 44 of all genes heterozygous for 1 or more
  variants
• Importance
• Inter-individual variations may be 3-4 fold
  higher than previously estimated (99.5 vs.
  99.9)

66
The Practice of Bioinformatics

• Reference
• Duarte N et al. Proc Natl Acad Sci U S A. 2007
  Feb 6104(6)1777-82. UC San Diego
• Title
• Global reconstruction of the human metabolic
  network based on genomic and bibliomic data.
• Aim
• Develop a computationally tractable, complete map
  of human metabolism
• Methods
• Combine genome annotations of complete human
  genome with 50 years of published literature
  (bibliome) on human metabolic pathways.

67
Bioinformatics Practice of Bioinformatics

• Reference
• Duarte N et al. Proc Natl Acad Sci U S A. 2007
  Feb 6104(6)1777-82.
• Results
• Systems biology project to create in silico model
  of all metabolic pathways in humans, and their
  genetic determinants
• Mathematical network analysis of resulting
  relationships show biological insights about
  intracellular compartmentalization (e.g., drug
  accessibility) and many gaps in understanding of
  relationships among metabolic pathways
• Importance
• An example of new systems biology tools that
  combine mathematical analysis techniques with
  knowledge derived from the published literature
• Traditional intermediary metabolism pathways
  (e.g., Sigma chart of cell) have many unexplained
  gaps

68
The Practice of Bioinformatics

• Reference
• Lim WK et al. Bioinformatics. 2007 Jul
  123(13)i282-8.Columbia Univ.
• Title
• Comparative analysis of microarray normalization
  procedures effects on reverse engineering gene
  networks.
• Aim
• Develop a more appropriate method for normalizing
  gene expression data for reconstructing gene
  networks
• Methods
• Comparison of commonly used algorithms for
  rendering data from different Affymetrix genechip
  experiments comparable

69
Bioinformatics Practice of Bioinformatics

• Reference
• Lim WK et al. Bioinformatics. 2007 Jul
  123(13)i282-8.
• Results
• Genechips designed for pairwise comparison of
  gene expression values. Inferring complex
  network relationships is an off-label use that
  can be affected by methodologic errors of
  normalization
• A better normalization algorithm developed at
  Columbias DBMI is presented
• Importance
• Mathematics of high dimensionality data from
  genechips is complex
• Systems biology requires careful attention to
  making data from multiple experiments comparable

70
The Practice of Bioinformatics

• Reference
• Bandeira et al. Proc Natl Acad Sci U S A. 2007
  Apr 10104(15)6140-5. UC San Diego
• Title
• Protein identification by spectral networks
  analysis.
• Aim
• Develop a better method for interpretation of
  mass spectroscopy signals for proteomics
• Methods
• Use modified unmodified versions of the same
  peptide to improve speed and efficiency of
  protein identification

71
Bioinformatics Practice of Bioinformatics

• Reference
• Bandeira et al. Proc Natl Acad Sci U S A. 2007
  Apr 10104(15)6140-5.
• Results
• Converts protein identification from exhaustive
  database searching problem to fast pattern
  matching problem
• Importance
• Proteomics is more complex than genomics (25K
  genes generate 400K proteins) and computationally
  challenging
• Representative of novel algorithms to rapidly
  identify proteins affected by post-translational
  modification

72
Computational Biology and Bioinformatics

• Questions and Comments

73
Top Ten List of Notable Events in the Past 12
months
74
Top Ten Events

• 10 Legislation mandates reporting of results
  in Clinicaltrials.gov 12/2006

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76
Top Ten Events

• 10 Legislation mandates reporting of results
  in Clinicaltrials.gov 12/2006
• 9 Public access to genome-phenome correlation
  data begins 10/1/2007 NCBI dbGAP database
  online

77
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Top Ten Events

• 10 Legislation mandates reporting of results
  in Clinicaltrials.gov 12/2006
• 9 Public access to genome-phenome correlation
  data begins 10/1/2007 NCBI dbGAP database
  online
• 8 Patient Safety Institute founded in 2001 in
  response to IOM To Error is Human report
  fails

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80
7 International Terminology Standards
Development Organization Formed April 26, 2007
81
Top Ten Events

• 10 Legislation mandates reporting of results
  in Clinicaltrials.gov 12/2006
• 9 Public access to genome-phenome correlation
  data begins 10/1/2007 NCBI dbGAP database
  online
• 8 Patient Safety Institute founded in 2001 in
  response to IOM To Error is Human report
  fails
• 7 International Terminology Standards
  Development Organization Formed
• 6 AMIA clout and visibility increases

82
AMIA RD funding growthGrants and Contracts
(gt50K)
83
AMIA VisibilityMedia Citations
84
Top Ten Events

• 10 Legislation mandates reporting of results
  in Clinicaltrials.gov 12/2006
• 9 Public access to genome-phenome correlation
  data begins 10/1/2007 NCBI dbGAP database
  online
• 8 Patient Safety Institute founded in 2001 in
  response to IOM To Error is Human report
  fails
• 7 International Terminology Standards
  Development Organization Formed
• 6 AMIA clout and visibility increases
• 5 NIH redefines scope of CTSA program

85
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86
Top Ten Events

• 10 Legislation mandates reporting of results
  in Clinicaltrials.gov 12/2006
• 9 Public access to genome-phenome correlation
  data begins 10/1/2007 NCBI dbGAP database
  online
• 8 Patient Safety Institute founded in 2001 in
  response to IOM To Error is Human report
  fails
• 7 International Terminology Standards
  Development Organization Formed
• 6 AMIA clout and visibility increases
• 5 NIH redefines scope of CTSA program
• 4 Publication of J. Craig Venters DNA
  sequence

87
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88
Top Ten Events

• 10 Legislation mandates reporting of results
  in Clinicaltrials.gov 12/2006
• 9 Public access to genome-phenome correlation
  data begins 10/1/2007 NCBI dbGAP database
  online
• 8 Patient Safety Institute founded in 2001 in
  response to IOM To Error is Human report
  fails
• 7 International Terminology Standards
  Development Organization Formed
• 6 AMIA clout and visibility increases
• 5 NIH redefines scope of CTSA program
• 4 Publication of J. Craig Venters DNA
  sequence
• 3 ONC begins plan to transition AHIC to
  private sector

89
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90
Top Ten Events

• 10 Legislation mandates reporting of results
  in Clinicaltrials.gov 12/2006
• 9 Public access to genome-phenome correlation
  data begins 10/1/2007 NCBI dbGAP database
  online
• 8 Patient Safety Institute founded in 2001 in
  response to IOM To Error is Human report
  fails
• 7 International Terminology Standards
  Development Organization Formed
• 6 AMIA clout and visibility increases
• 5 NIH redefines scope of CTSA program
• 4 Publication of J. Craig Venters DNA
  sequence
• 3 ONC begins plan to transition AHIC to
  private sector
• 2 Microsoft and Google announce plans for
  Personal Health Records

91
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92
And the 1 top event of 2007 is
93
Top Ten Events

• 10 Legislation mandates reporting of results
  in Clinicaltrials.gov 12/2006
• 9 Public access to genome-phenome correlation
  data begins 10/1/2007 NCBI dbGAP database
  online
• 8 Patient Safety Institute founded in 2001 in
  response to IOM To Error is Human report
  fails
• 7 International Terminology Standards
  Development Organization Formed
• 6 AMIA clout and visibility increases
• 5 NIH redefines scope of CTSA program
• 4 Publication of J. Craig Venters DNA
  sequence
• 3 ONC begins plan to transition AHIC to
  private sector
• 2 Microsoft and Google announce plans for
  Personal Health Records
• 1 CMS begins program to reward small practices
  for using EHRs

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95
The Year in Review Summary

• We is confronted by an insurmountable tidal
  wave of opportunity

Pogo
96
Content for this session is athttp//dbmichair.
mc.vanderbilt.edu/amia2007/including citation
lists and linksand this PowerPoint