Advances in genotyping technology have, over the past decade, enabled the focused search for common genetic variation associated with human diseases and traits. With the recently increased availability of detailed phenotypic data from electronic health records and epidemiological studies, the impact of one or more genetic variants on the phenome is starting to be characterized both in clinical and population-based settings using phenome-wide association studies (PheWAS). These studies reveal a number of challenges that will need to be overcome to unlock the full potential of PheWAS for the characterization of the complex human genome-phenome relationship.

Unravelling the human genome-phenome relationship using phenome-wide association studies

Background: The national mandate for health systems to transition from ICD-9-CM to ICD-10-CM in October 2015 has an impact on research activities. Clinical phenotypes defined by ICD-9-CM codes need to be converted to ICD-10-CM, which has nearly four times more codes and a very different structure than ICD-9-CM. Methods:  We used the Centers for Medicare & Medicaid Services (CMS) General Equivalent Maps (GEMs) to translate, using four different methods, condition-specific ICD-9-CM code sets used for pragmatic trials (n=32) into ICD-10-CM. We calculated the recall, precision, and F‑score of each method. We also used the ICD-9-CM and ICD-10-CM value sets defined for electronic quality measure as an additional evaluation of the mapping methods. Results:  The forward-backward mapping (FBM) method had higher precision, recall and F‑score metrics than simple forward mapping (SFM). The more aggressive secondary (SM) and tertiary mapping (TM) methods resulted in higher recall but lower precision. For clinical phenotype definition, FBM was the best (F=0.67), but was close to SM (F=0.62) and TM (F=0.60), judging on the F‑scores alone. The overall difference between the four methods was statistically significant (one-way ANOVA, F=5.749, p=0.001). However, pairwise comparisons between FBM, SM, and TM did not reach statistical significance. A similar trend was found for the quality measure value sets. Discussion:  The optimal method for using the GEMs depends on the relative importance of recall versus precision for a given use case. It appears that for clinically distinct and homogenous conditions, the recall of FBM is sufficient. The performance of all mapping methods was lower for heterogeneous conditions. Since code sets used for phenotype definition and quality measurement can be very similar, there is a possibility of cross-fertilization between the two activities. Conclusion:  Different mapping approaches yield different collections of ICD-10-CM codes. All methods require some level of human validation.

Preparing for the ICD-10-CM Transition: Automated Methods for Translating ICD Codes in Clinical Phenotype Definitions

Purpose To describe the consistency in the frequency of 5 health outcomes across the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) and Tenth Revision, Clinical Modification (ICD-10-CM) eras in the US. Methods We examined the incidence of 3 acute conditions (acute myocardial infarction [AMI], angioedema, ischemic stroke) and the prevalence of 2 chronic conditions (diabetes, hypertension) during the final 5 years of the ICD-9-CM era (January 2010-September 2015) and the first 15 months of the ICD-10-CM era (October 2015-December 2016) in 13 electronic health care databases in the Sentinel System. For each health outcome reviewed during the ICD-10-CM era, we evaluated 4 definitions, including published algorithms derived from other countries, as well as simple-forward, simple-backward, and forward-backward mapping using the General Equivalence Mappings. For acute conditions, we also compared the incidence between April to December 2014 and April to December 2016. Results The analyses included data from approximately 172 million health plan members. While the incidence or prevalence of AMI and hypertension performed similarly across the 2 eras, the other 3 outcomes did not demonstrate consistent trends for some or all the ICD-10-CM definitions assessed. Conclusions When using data from both the ICD-9-CM and ICD-10-CM eras, or when using results from ICD-10-CM data to compare to results from ICD-9-CM data, researchers should test multiple ICD-10-CM outcome definitions as part of sensitivity analysis. Ongoing assessment of the impact of ICD-10-CM transition on identification of health outcomes in US electronic health care databases should occur as more data accrue.

Early impact of the ICD-10-CM transition on selected health outcomes in 13 electronic health care databases in the United States.

Background Suboptimal weight gain during pregnancy is a potentially modifiable risk factor. We aimed to investigate the association between suboptimal gestational weight gain and severe adverse birth outcomes by pre-pregnancy body mass index (BMI) categories, including obesity class I to III. Methods and findings We conducted a population-based study of pregnant women with singleton hospital births in Washington State, US, between 2004 and 2013. Optimal, low, and excess weight gain in each BMI category was calculated based on weight gain by gestational age as recommended by the American College of Obstetricians and Gynecologists and the Institute of Medicine. Primary composite outcomes were (1) maternal death and/or severe maternal morbidity (SMM) and (2) perinatal death and/or severe neonatal morbidity. Logistic regression was used to obtain adjusted odds ratios (AORs) and 95% confidence intervals. Overall, 722,839 women with information on pre-pregnancy BMI were included. Of these, 3.1% of women were underweight, 48.1% had normal pre-pregnancy BMI, 25.8% were overweight, and 23.0% were obese. Only 31.5% of women achieved optimal gestational weight gain. Women who had low weight gain were more likely to be African American and have Medicaid health insurance, while women with excess weight gain were more likely to be non-Hispanic white and younger than women with optimal weight gain in each pre-pregnancy BMI category. Compared with women who had optimal weight gain, those with low gestational weight gain had a higher rate of maternal death, 7.97 versus 2.63 per 100,000 (p = 0.027). In addition, low weight gain was associated with the composite adverse maternal outcome (death/SMM) in women with normal pre-pregnancy BMI and in overweight women (AOR 1.12, 95% CI 1.04–1.21, p = 0.004, and AOR 1.17, 95% CI 1.04–1.32, p = 0.009, respectively) compared to women in the same pre-pregnancy BMI category who had optimal weight gain. Similarly, excess gestational weight gain was associated with increased rates of death/SMM among women with normal pre-pregnancy BMI (AOR 1.20, 95% CI 1.12–1.28, p < 0.001) and obese women (AOR 1.12, 95% CI 1.01–1.23, p = 0.019). Low gestational weight gain was associated with perinatal death and severe neonatal morbidity regardless of pre-pregnancy BMI, including obesity classes I, II, and III, while excess weight gain was associated with severe neonatal morbidity only in women who were underweight or had normal BMI prior to pregnancy. Study limitations include the ascertainment of pre-pregnancy BMI using self-report, and lack of data availability for the most recent years. Conclusions In this study, we found that most women do not achieve optimal weight gain during pregnancy. Low weight gain was associated with increased risk of severe adverse birth outcomes, and in particular with maternal death and perinatal death. Excess gestational weight gain was associated with severe adverse birth outcomes, except for women who were overweight prior to pregnancy. Weight gain recommendations for this group may need to be reassessed. It is important to counsel women during pregnancy about specific risks associated with both low and excess weight gain.

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Association between gestational weight gain and severe adverse birth outcomes in Washington State, US: A population-based retrospective cohort study, 2004-2013.

Beginning October 2015, the Center for Medicare and Medicaid Services will require medical providers to use the vastly expanded International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) system. Despite wide availability of information and mapping tools for the next generation of the ICD classification system, some of the challenges associated with transition from ICD-9-CM to ICD-10-CM are not well understood. To quantify the challenges faced by emergency physicians, we analyzed a subset of a 2010 Illinois Medicaid database of emergency department ICD-9-CM codes, seeking to determine the accuracy of existing mapping tools in order to better prepare emergency physicians for the change to the expanded ICD-10-CM system. We found that 27% of 1830 codes represented convoluted multidirectional mappings. We then analyzed the convoluted transitions and found that 8% of total visit encounters (23% of the convoluted transitions) were clinically incorrect. The ambiguity and inaccuracy of these mappings may impact the workflow associated with the translation process and affect the potential mapping between ICD codes and Current Procedural Codes, which determine physician reimbursement.

The complexity and challenges of the International Classification of Diseases, Ninth Revision, Clinical Modification to International Classification of Diseases, 10th Revision, Clinical Modification transition in EDs

Young Min Yang

Papers

Challenges and remediation for Patient Safety Indicators in the transition to ICD-10-CM

Metrics and tools for consistent cohort discovery and financial analyses post-transition to ICD-10-CM