Post-Treatment Mortality After Surgery and Stereotactic Body Radiotherapy for Early-Stage Non-Small-Cell Lung Cancer

Purpose In early-stage non-small cell lung cancer (NSCLC), post-treatment mortality may influence the comparative effectiveness of surgery and stereotactic body radiotherapy (SBRT), with implications for shared decision making among high-risk surgical candidates. We analyzed early mortality after these interventions using the National Cancer Database. Patients and Methods We abstracted patients with cT1-T2a, N0, M0 NSCLC diagnosed between 2004 and 2013 undergoing either surgery or SBRT. Thirty-day and 90-day post-treatment mortality rates were calculated and compared using Cox regression and propensity score-matched analyses. Results We identified 76,623 patients who underwent surgery (78% lobectomy, 20% sublobar resection, 2% pneumonectomy) and 8,216 patients who received SBRT. In the unmatched cohort, mortality rates were moderately increased with surgery versus SBRT (30 days, 2.07% v 0.73% [absolute difference (Δ), 1.34%]; P < .001; 90 days, 3.59% v 2.93% [Δ, 0.66%]; P < .001). Among the 27,200 propensity score-matched patients, these differences increased (30 days, 2.41% v 0.79% [Δ, 1.62%]; P < .001; 90 days, 4.23% v 2.82% [Δ, 1.41%]; P < .001). Differences in mortality between surgery and SBRT increased with age, with interaction P < .001 at both 30 days and 90 days (71 to 75 years old: 30-day Δ, 1.87%; 90-day Δ, 2.02%; 76 to 80 years old: 30-day Δ, 2.80%; 90-day Δ, 2.59%; > 80 years old: 30-day Δ, 3.03%; 90-day Δ, 3.67%; all P ≤ .001). Compared with SBRT, surgical mortality rates were higher with increased extent of resection (30-day and 90-day multivariate hazard ratio for mortality: sublobar resection, 2.85 and 1.37; lobectomy, 3.65 and 1.60; pneumonectomy, 14.5 and 5.66; all P < 0.001). Conclusion Differences in 30- and 90-day post-treatment mortality between surgery and SBRT increased as a function of age, with the largest differences in favor of SBRT observed among patients older than 70 years. These representative mortality data may inform shared decision making among patients with early-stage NSCLC who are eligible for both interventions.

Patterns of Fractionation and Boost Usage in Adjuvant External Beam Radiotherapy for Ductal Carcinoma in Situ in the United States

BACKGROUND

While the roles of hypofractionated (HFxn) radiotherapy and lumpectomy boost in the adjuvant management of invasive breast cancer are supported by the results of clinical trials, randomized data supporting their use for ductal carcinoma in situ (DCIS) are forthcoming. We sought to evaluate current national trends and identify factors associated with HFxn and boost usage using the National Cancer Database.

PATIENTS AND METHODS

We queried the National Cancer Database for women diagnosed with DCIS from 2004 to 2014 undergoing external beam radiotherapy after breast conservation surgery. Patients were categorized as receiving either conventional fractionation (CFxn) or HFxn and as either receiving or not receiving a boost. Multiple logistic regression was performed to identify demographic, clinical, and treatment factor associations.

RESULTS

A total of 101,615 women were identified, with 87,641 (86.2%) receiving CFxn, 13,974 (13.8%) receiving HFxn, and most patients in each group (84.9% and 57.7%, respectively) receiving a boost. Implementation of HFxn increased from 4.3% in 2004 to 33.0% in 2014, and the use of a boost declined from 83.3% to 74.6%. HFxn receipt was independently associated with later year of diagnosis, older age, higher income, greater distance from treatment facility, greater facility volume, academic facility type, Western residence, smaller lesions, and nonreceipt of a boost. Factors associated with boost receipt included earlier year of diagnosis, younger age, higher income, community facility type, adverse pathologic features, and nonreceipt of HFxn.

CONCLUSION

Although CFxn with a boost remains the most common external beam radiotherapy strategy for DCIS, implementation of HFxn without a boost appears to be increasing. Practice patterns at present seem to be driven by guidelines for invasive breast cancer and nonclinical factors.

Survival impact of pre-treatment neutrophils on oropharyngeal and laryngeal cancer patients undergoing definitive radiotherapy

Background

Squamous cell carcinoma of the head and neck (HNSCC) represents an array of disease processes with a generally unfavorable prognosis. Inflammation plays an important role in tumor development and response to therapy. We performed a retrospective analysis of HNSCC patients to explore the relationship of the lymphocyte and neutrophil counts, the neutrophil-to-lymphocyte ratio (NLR) overall survival (OS), cancer-specific survival (CSS), local control (LC) and distant control (DC).

Materials/methods

All patients received definitive treatment for cancers of the oropharynx or larynx between 2006–2015. Neutrophil and lymphocyte counts were collected pre-, during-, and post-treatment. The correlations of patient, tumor, and biological factors to OS, CSS, LC and DC were assessed.

Results

196 patients met our inclusion criteria; 171 patients were Stage III or IV. Median follow-up was 2.7 years. A higher neutrophil count at all treatment time points was predictive of poor OS with the pre-treatment neutrophil count and overall neutrophil nadir additionally predictive of DC. Higher pre-treatment and overall NLR correlated to worse OS and DC, respectively.

Conclusion

A higher pre-treatment neutrophil count correlates to poor OS, CSS and DC. Lymphocyte counts were not found to impact survival or tumor control. Higher pre-treatment NLR is prognostic of poor OS.

Electronic supplementary material

The online version of this article (doi:10.1186/s12967-017-1268-7) contains supplementary material, which is available to authorized users.

Patterns of Care for Patients With Early-Stage Glottic Cancer Undergoing Definitive Radiation Therapy: A National Cancer Database Analysis

PURPOSE

To characterize practice patterns, including temporal trends, in fractionation schedules among patients in the United States undergoing definitive radiation therapy for early-stage glottic cancer and to compare overall survival outcomes between fractionation schedules.

METHODS AND MATERIALS

We queried the National Cancer Database for patients with TisN0M0, T1N0M0, or T2N0M0 squamous cell carcinoma of the glottic larynx diagnosed between 2004 and 2012 and undergoing definitive radiation therapy. Dose per fraction was calculated to define cohorts undergoing conventional fractionation (CFxn) and hypofractionation (HFxn). Logistic regression was performed to identify predictors of receiving HFxn, and Cox regression was used to determine predictors of death. One-to-one propensity score matching was then used to compare survival between fractionation schedules.

RESULTS

The study included 10,539 patients, with 6576 undergoing CFxn and 3963 undergoing HFxn. Patients with T1 disease comprised a majority of each cohort. Use of HFxn increased significantly over the period studied (P<.001), but even in the final year, nearly one-half of patients continued to receive CFxn. Receipt of HFxn was also independently associated with higher income and facility types other than community cancer programs on logistic regression. On multivariate Cox regression, HFxn was associated with improved survival (hazard ratio [HR] for death, 0.90; 95% confidence interval [CI], 0.83-0.97; P=.008), a finding redemonstrated on univariate Cox regression among a well-matched cohort after propensity score matching (HR, 0.88; 95% CI, 0.80-0.96; P=.003). Subgroup Cox multivariate analysis demonstrated a significant survival advantage with HFxn among patients with T1 disease (HR, 0.90; 95% CI, 0.81-0.99; P=.042) but a nonsignificant benefit among those with Tis (HR, 0.86; 95% CI, 0.57-1.30; P=.472) or T2 (HR, 0.88; 95% CI, 0.76-1.02; P=.099) disease.

CONCLUSIONS

Use of HFxn is increasing and is associated with improved survival over CFxn. Our findings support the broadened use of HFxn for patients with early-stage glottic cancer undergoing definitive radiation therapy.

Survival impact of induction chemotherapy in advanced head and neck cancer: A National Cancer Database analysis

BACKGROUND

Adding induction chemotherapy to concurrent chemotherapy and radiotherapy (RT) has generally not improved the overall survival (OS) in randomized trials of patients with head and neck cancer. This failure may stem from inadequate power or inappropriate patient selection, prompting this National Cancer Data Base analysis.

METHODS

8031 patients with T4 or N2b to N3 disease undergoing RT and chemotherapy were divided into induction chemotherapy and concurrent chemotherapy cohorts. Multivariate analysis was used to explore the association of treatment with survival and to identify predictors of radiation dose.

RESULTS

On multivariate analysis incorporating sociodemographic and clinical variables, survival of the induction chemotherapy cohort was not significantly different from that of the concurrent cohort (hazard ratio [HR], 0.96; 95% confidence interval [CI], 0.88-1.05; p = .35), nor on subgroup analyses of advanced disease. Multivariate analysis demonstrated increased odds of receiving <66 Gy among the patients in the induction chemotherapy cohort (p < .01).

CONCLUSION

Induction chemotherapy subjects experienced no survival advantage over concurrent chemotherapy subjects but were more likely to receive lower RT doses. © 2017 Wiley Periodicals, Inc. Head Neck 39: 1113-1121, 2017.

A comparison of overall survival for patients with T4 larynx cancer treated with surgical versus organ-preservation approaches: A National Cancer Data Base analysis

BACKGROUND

Although laryngectomy is the treatment of choice for patients with T4 larynx cancer, many patients are unable or unwilling to undergo laryngectomy and instead pursue larynx-preservation strategies combining radiotherapy (RT) and chemotherapy. Herein, the authors analyzed the National Cancer Data Base to evaluate overall survival (OS) between patients treated with surgical and organ-preserving modalities.

METHODS

The National Cancer Data Base was queried for patients diagnosed from 2004 through 2012 with T4M0 laryngeal cancer who underwent either laryngectomy (surgery) with adjuvant RT (SRT), chemotherapy starting concurrently within 7 days of RT (CCRT), or multiagent induction chemotherapy starting 43 to 98 days before RT (ICRT). Multivariate analysis and propensity score matching were used to explore the association between the intervention and OS. Recursive partitioning analysis was performed to identify groups benefiting from particular modalities.

RESULTS

A total of 1559 patients who underwent SRT, 1597 patients who underwent CCRT, and 386 patients who underwent ICRT were included. Adjusting for covariates, CCRT was found to be associated with inferior OS compared with SRT (hazard ratio [HR], 1.55; 95% confidence interval [95% CI], 1.41-1.70 [P<.01]) and with ICRT (HR, 1.25; 95% CI, 1.07-1.45 [P<.01]). OS among the patients treated with SRT did not appear to differ significantly from that of the ICRT cohort (HR, 0.87; 95% CI, 0.73-1.03 [P =  0.10]), a finding confirmed with propensity score matching. Recursive partitioning analysis identified no subset of patients that derived an OS benefit from either approach over the other.

CONCLUSIONS

OS among patients undergoing SRT was found to be superior to that of patients treated with CCRT but did not significantly differ from that of those undergoing ICRT. Because these intriguing findings require validation, SRT should remain the standard of care for patients with this disease. However, organ preservation with ICRT may be a reasonable alternative in certain patients. Cancer 2017;123:600-608. © 2016 American Cancer Society.

Is sex an independent prognostic factor in esthesioneuroblastoma?

OBJECTIVE

To determine if sex independently affects presentation and disease-specific survival (DSS) in patients with esthesioneuroblastoma (ENB).

STUDY DESIGN

A case-control study from the Surveillance Epidemiology and End Results (SEER) data base.

METHODS

The assessment identified 611 patients in the SEER data base who were diagnosed with ENB from 1988 to 2010. Data on race, ethnicity, age at diagnosis, sex, histologic grade, radiation treatment status, and surgical treatment status of patients with ENB from 1988 to 2010 were extracted. By using tumor extension data, the modified Kadish stage of each case was determined. The modified Kadish system was able to successfully classify 547 of 611 tumors from 1988 to 2010. Histologic grade, modified Kadish stage and DSS of male patients was compared with the DSS of female patients.

RESULTS

Demographic data showed that male patients presented with a significantly higher grade (p < 0.05) and a trend toward a higher stage (p = 0.08). With unmatched data, male patients had significantly worse DSS than female patients (p < 0.05). After case-matching, the difference between the DSS for male versus female patients was no longer significant.

CONCLUSIONS

Male patients with ENB seemed to have significantly worse DSS at 10 years than female patients. This disparity seems to be due to higher grade and stage in male patients at presentation. After accounting for these two factors, the prognosis of male patients was not found to be significantly different from that of female patients.

Cancer screening rates in individuals with different life expectancies

IMPORTANCE

Routine cancer screening has unproven net benefit for patients with limited life expectancy.

OBJECTIVE

To examine the patterns of prostate, breast, cervical, and colorectal cancer screening in the United States in individuals with different life expectancies.

DESIGN, SETTING, AND PARTICIPANTS

Data from the population-based National Health Interview Survey (NHIS) from 2000 through 2010 were used and included 27 404 participants aged 65 years or older. Using a validated mortality index specific for NHIS, participants were grouped into those with low (<25%), intermediate (25%-49%), high (50%-74%), and very high (≥75%) risks of 9-year mortality.

MAIN OUTCOMES AND MEASURES

Rates of prostate, breast, cervical, and colorectal cancer screening.

RESULTS

In participants with very high mortality risk, 31% to 55% received recent cancer screening, with prostate cancer screening being most common (55%). For women who had a hysterectomy for benign reasons, 34% to 56% had a Papanicolaou test within the past 3 years. On multivariate analysis, very high vs low mortality risk was associated with less screening for prostate (odds ratio [OR], 0.65 [95% CI, 0.50-0.85]), breast (OR, 0.43 [95% CI, 0.35-0.53]), and cervical (OR, 0.50 [95% CI, 0.36-0.70]) cancers. There was less screening for prostate and cervical cancers in more recent years compared with 2000, and there was no significant interaction between calendar year and mortality risk for any cancer screening (P > .05 for all cancers). Our sensitivity analysis showed that screening was also common in individuals with less than 5-year life expectancy.

CONCLUSIONS AND RELEVANCE

A substantial proportion of the US population with limited life expectancy received prostate, breast, cervical, and colorectal cancer screening that is unlikely to provide net benefit. These results suggest that overscreening is common in both men and women, which not only increases health care expenditure but can lead to net patient harm.

Recommended patient-reported core set of symptoms to measure in prostate cancer treatment trials

The National Cancer Institute (NCI) Symptom Management and Health-Related Quality of Life Steering Committee convened four working groups to recommend core sets of patient-reported outcomes to be routinely incorporated in clinical trials. The Prostate Cancer Working Group included physicians, researchers, and a patient advocate. The group's process included 1) a systematic literature review to determine the prevalence and severity of symptoms, 2) a multistakeholder meeting sponsored by the NCI to review the evidence and build consensus, and 3) a postmeeting expert panel synthesis of findings to finalize recommendations. Five domains were recommended for localized prostate cancer: urinary incontinence, urinary obstruction and irritation, bowel-related symptoms, sexual dysfunction, and hormonal symptoms. Four domains were recommended for advanced prostate cancer: pain, fatigue, mental well-being, and physical well-being. Additional domains for consideration include decisional regret, satisfaction with care, and anxiety related to prostate cancer. These recommendations have been endorsed by the NCI for implementation.

Is sex an independent prognostic factor in cutaneous head and neck melanoma?

OBJECTIVES/HYPOTHESIS

To determine if sex independently affects disease-specific survival (DSS) in patients with cutaneous head and neck melanoma.

STUDY DESIGN

Retrospective analysis of a large population database.

METHODS

Our study included patients in the Surveillance, Epidemiology, and End Results database with cutaneous head and neck melanoma diagnosed from 2004 to 2009. Any cases with a history of previous malignancy or with multiple primaries were excluded. We obtained data on stage, race, age at diagnosis, radiological treatment status, and surgical treatment status. Our analysis consisted of a Kaplan-Meier analysis of DSS by sex [correction made here after initial online publication] that was supported by a multivariate Cox regression of all significant variables studied.

RESULTS

There were 13,507 patients identified with cutaneous head and neck melanoma who were diagnosed between 2004 and 2009. We observed that female patients had a better prognosis than their male counterparts, with 5-year DSS of 90.40% (95% confidence interval [CI], 89.03%-91.72%) and 87.10% (95% CI, 86.12%-88.08%), respectively. Multivariable analysis demonstrated a statistically significant decrease in disease-specific hazard ratio due to female sex independent of stage, treatment, age, or race.

CONCLUSIONS

Our study concludes that female sex is an independent prognostic factor for cutaneous head and neck melanoma. We demonstrated better 5-year DSS in female compared to male patients. Better prognosis could be due to multiple factors including differing hair, levels of sun exposure, and advanced male age.

LEVEL OF EVIDENCE

2b.

Analysis of Racial Survival Disparities in Head and Neck Cancer by Site of Primary Tumor

Objectives:

Head and neck cancer carries a significant survival disparity by race and site of primary tumor. We performed survival analysis to determine how racial survival disparities differ by site.

Methods:

We selected 34,182 patients from the Surveillance, Epidemiology, and End Results (SEER) database with head and neck cancer (HNC) diagnosed from 2004-2009. Eighty-three point nine percent were white, 11.4% black, 4.28% Asian or Pacific Islander, and 0.36% American Indian. All patients with >1 primary and primaries outside the upper aero-digestive tract were excluded. American Joint Committee on Cancer (AJCC) staging in SEER was recorded with stages I and II as early stage, and stages III and IV as late stage. Hazardous ratio were calculated with and without stage as covariates.

Results:

Stage independent: hazard ratio (HR) for black vs. white survival was 1.637 (95% confidence interval [CI] = 1.455-1.842, P <.001) for mouth, 2.402 (95% CI = 2.182-2.644, P <.001) for oropharynx, 1.382 (95% CI = 1.275-1.530, P =<.001) for larynx, and 1.563 (95% CI = 01.337-1.827, P = <.001) for hypopharynx. Stage dependent: HR of 1.297 (95% CI = 1.152-1.460, P = <.001) for mouth, 2.349 (95% CI = 2.134-2.586, P <.001) for oropharynx, 1.124 (95% CI = 1.014-1.246, P = .025) for larynx, and 1.541 (95% CI = 1.318-1.802, P =<.001) for hypopharynx.

Conclusions:

We found racial survival disparities in HNC for all sites, with differing reasons by location. The mouth and larynx’s disparity is significantly affected by stage at presentation, but primaries of the oropharynx are not. Therefore, poor tumor recognition is a major reason for black survival disparities in early diagnostic areas. However, in inferior upper aero-digestive tract lesions the disparity is not due to a difference in tumor recognition and likely stems from differences in treatment or risk factors such as human papillomavirus status.

Racial differences in time from prostate cancer diagnosis to treatment initiation: a population-based study

BACKGROUND

Timely delivery of care has been identified by the Institute of Medicine as an indicator for quality health care, and treatment delay is a potentially modifiable obstacle that can contribute to the disparities among African American (AA) and Caucasian patients in prostate cancer recurrence and mortality. Using the Surveillance, Epidemiologic and End Results (SEER)-Medicare linked database, we compared time from diagnosis to treatment in AA and Caucasian prostate cancer patients.

METHODS

A total of 2506 AA and 21,454 Caucasian patients diagnosed with localized prostate cancer from 2004 through 2007 and treated within 12 months were included. Linear regression was used to assess potential differences in time to treatment between AA and Caucasian patients, after adjusting for sociodemographic and clinical covariates.

RESULTS

Time from diagnosis to definitive (prostatectomy and radiation) treatment was longer for AA patients in all risk groups, and most pronounced in high-risk cancer (96 versus 105 days, P < .001). On multivariate analysis, racial differences to any and definitive treatment persisted (β = 7.3 and 7.6, respectively, for AA patients). Delay to definitive treatment was longer in high-risk (versus low-risk) disease and in more recent years.

CONCLUSIONS

AA patients with prostate cancer experienced longer time from diagnosis to treatment than Caucasian patients with prostate cancer. AA patients appear to experience disparities across all aspects of this disease process, and together these factors in receipt of care plausibly contribute to the observed differences in rates of recurrence and mortality among AA and Caucasian patients with prostate cancer.

Prevalence of cardiovascular disease (CVD) risk factors and receipt of preventive care among prostate cancer (CaP) survivors in the United States

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Background: CVD is a major cause of mortality in CaP survivors. Prior claims-based studies have reported underutilization of preventive care in cancer survivors, but most CVD preventive care items are not available in claims data. We directly examined the prevalence of CVD risk factors and receipt of care in patients with these risk factors in two population-based data sources: National Health and Nutrition Examination Survey (NHANES) and National Health Interview Survey (NHIS) – both commonly used to examine patterns of care in the US. Methods: 2,938 (NHANES) and 452 (NHIS) men with CaP diagnosed from 1999 to 2011 were included. Statistical analysis accounted for sampling weight, and was stratifiedby Caucasian (CA) vs. non-CA. Results: CVD risk factors are highly prevalent (Table), and appear more so in non-Caucasian survivors. Further, 32% of survivors reported history of actual CVD (prior stroke, myocardial infarction, angina, or coronary heart disease). Overall, the majority of survivors receive preventive care. 89%of CA and non-CA survivors visited a primary care physician in the past 1 year. Among survivors with hypertension or hyperlipidemia, >80% received blood pressure or cholesterol checks within past 1 year. Rates of tobacco cessation and exercise were lower. Conclusions: CVD and associated risk factors are prevalent in CaP survivors. However, the majority of these survivors visit a primary care physician and receive CVD preventive care. [Table: see text]

Prostate-specific antigen (PSA) screening in the United States: Patterns of use and PSA outcomes in screened versus unscreened men

4658

Background: PSA screening is a subject of substantial controversy. We examined patterns of PSA screening using a recent cohort from the population-based National Health and Nutrition Examination Survey (NHANES) study and compared PSA levels of previously screened vs. never screened men. Methods: NHANES is a cross-sectional study which collects health-related information (including cancer screening history, family history and socioeconomic variables) and blood samples from nationally representative samples of the US population. We included 2,078 previously screened men and 1,902 never screened men surveyed from 2003-8. Statistical analysis accounted for sampling weights. Results: 25% of men age 40-49 years had prior PSA screening; 56% age 50-59, and 72% age 60-69. Screening rates were higher for men with family history (68% vs. 50% no history, p<.001), health insurance (58% vs. 21% no insurance, p<.001), and Caucasians (59% vs. 44% non-Caucasian, p<.001). No significant differences were seen in the PSA values of screened vs. never screened men stratified by age (Table), or by race/ethnicity, insurance status, or family history. Conclusions: Rates of PSA screening in the US differ by age, family history, race/ethnicity and insurance status. However, no significant differences were seen in PSA values of screened vs. unscreened men, and very few patients under 60 years of age had PSA values ≥10. Despite questions about the appropriate role of PSA testing, population-based prostate cancer screening is routinely conducted among Caucasian and non-Caucasian men 50 years of age and older. [Table: see text]

Life expectancy (LE) and the receipt of conservative versus active treatment in men with prostate cancer (CaP): A population-based study

6032

Background: Prostate-specific antigen (PSA) screening increases the diagnosis of low-risk and potentially clinically insignificant CaP, which raises concern for possible overtreatment. The National Comprehensive Cancer Network (NCCN) guidelines recommend surveillance (conservative management) for patients with less than 10 years LE diagnosed with low-risk cancer. In contrast, NCCN recommends active treatment for high-risk CaP, the most aggressive form of this disease, irrespective of LE. We examine patterns of care in CaP patients in the Surveillance, Epidemiology and End Results (SEER) registry by LE. Methods: 152,578 men with non-metastatic CaP diagnosed from 2004-8 were included. Gleason, PSA, and clinical stage were used for risk-categorization per D’Amico criteria. The sample was dichotomized into men 76 years and younger (who have an average LE of 10 years or more based on the US Social Security Administration actuarial period life tables) vs. 77 years and older (less than 10 years average LE). Logistic regression models examined factors associated with each treatment modality. Results: 56% of patients age 77 and older with low-risk CaP received conservative management, and 44% active treatment (Table). However, conservative management was just as common in older patients with high-risk cancer (62%); 21% of younger patients with high-risk CaP also received conservative management. Multivariable analysis showed decreased use of conservative management over time in older patients (OR 0.78 for 2008 vs. 2004, 95%CI 0.71-.86, p<.001). African American race, being unmarried, and older age were also significantly associated with conservative management. Conclusions: There may be overtreatment of low-risk CaP patients age 77 and older, which is worsening in recent years. Correspondingly, there appears to be undertreatment of elderly patients with high-risk CaP, the most aggressive form of this disease. [Table: see text]

MICA: desktop software for comprehensive searching of DNA databases

Background

Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory.

Results

MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited.

Conclusion

MICA is suitable as a search engine for desktop DNA analysis software.